diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 66148dd..1db3d93 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ default_stages: [commit, manual]
 fail_fast: true
 repos:
     - repo: "https://github.com/commitizen-tools/commitizen"
-      rev: v2.39.1
+      rev: v2.40.0
       hooks:
           - id: commitizen
           - id: commitizen-branch
@@ -39,6 +39,7 @@ repos:
           - id: check-shebang-scripts-are-executable
           - id: check-symlinks
           - id: check-toml
+            exclude: broken_config_file\.toml
           - id: check-vcs-permalinks
           - id: check-xml
           - id: check-yaml
@@ -60,7 +61,7 @@ repos:
             entry: yamllint --strict --config-file .yamllint.yml
 
     - repo: "https://github.com/charliermarsh/ruff-pre-commit"
-      rev: "v0.0.229"
+      rev: "v0.0.230"
       hooks:
           - id: ruff
             args: ["--extend-ignore", "I001,D301,D401,PLR2004"]
diff --git a/README.md b/README.md
index f73a1d7..66abb37 100644
--- a/README.md
+++ b/README.md
@@ -33,16 +33,27 @@ The script provides a menu of available actions. Make as many changes as you req
 
 
 ### Configuration
-`obsidian-metadata` requires a configuration file at `~/.obsidian_metadata.toml`.  On first run, this file will be created.  Read the comments in this file to configure your preferences.  This configuration file contains the following information.
+`obsidian-metadata` requires a configuration file at `~/.obsidian_metadata.toml`.  On first run, this file will be created.  You can specify a new location for the configuration file with the `--config-file` option.
+
+To add additional vaults, copy the default section and add the appropriate information. The script will prompt you to select a vault if multiple exist in the configuration file
+
+Below is an example with two vaults.
 
 ```toml
-# Path to your obsidian vault
-vault = "/path/to/vault"
+["Vault One"] # Name of the vault.
 
-# Folders within the vault to ignore when indexing metadata
-exclude_paths = [".git", ".obsidian"]
+    # Path to your obsidian vault
+    path = "/path/to/vault"
+
+    # Folders within the vault to ignore when indexing metadata
+    exclude_paths = [".git", ".obsidian"]
+
+["Vault Two"]
+    path = "/path/to/second_vault"
+    exclude_paths = [".git", ".obsidian"]
 ```
 
+To bypass the configuration file and specify a vault to use at runtime use the `--vault-path` option.
 
 
 # Contributing
diff --git a/poetry.lock b/poetry.lock
index 6882a94..9391c20 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -699,7 +699,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 
@@ -707,7 +707,7 @@ python-versions = ">=3.7"
 name = "tomlkit"
 version = "0.11.6"
 description = "Style preserving TOML library"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -814,7 +814,7 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"]
 [metadata]
 lock-version = "1.1"
         python-versions = "^3.10"
-content-hash = "db4a41f0b94c3bf84fa548a6733da1cced1fedc2bdfdc6f80396dddbd5619bfd"
+content-hash = "acbde0d9374261931e4f12f4ed8fcbc543008f68c4aed0a6748280a3999b3394"
 
 [metadata.files]
 absolufy-imports = [
diff --git a/pyproject.toml b/pyproject.toml
index 97ebf6c..aa16354 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@
         rich        = "^13.2.0"
         ruamel-yaml = "^0.17.21"
         shellingham = "^1.4.0"
-        tomli       = "^2.0.1"
+        tomlkit     = "^0.11.6"
         typer       = "^0.7.0"
 
     [tool.poetry.group.test.dependencies]
diff --git a/src/obsidian_metadata/_config/__init__.py b/src/obsidian_metadata/_config/__init__.py
index d03444b..7674d15 100644
--- a/src/obsidian_metadata/_config/__init__.py
+++ b/src/obsidian_metadata/_config/__init__.py
@@ -1,5 +1,5 @@
 """Config module for obsidian frontmatter."""
 
-from obsidian_metadata._config.config import Config
+from obsidian_metadata._config.config import Config, VaultConfig
 
-__all__ = ["Config"]
+__all__ = ["Config", "VaultConfig"]
diff --git a/src/obsidian_metadata/_config/config.py b/src/obsidian_metadata/_config/config.py
index e70d771..16fe2d1 100644
--- a/src/obsidian_metadata/_config/config.py
+++ b/src/obsidian_metadata/_config/config.py
@@ -1,61 +1,52 @@
 """Instantiate the configuration object."""
 
-import re
-import shutil
+
 from pathlib import Path
+from textwrap import dedent
 from typing import Any
 
-import questionary
 import rich.repr
+import tomlkit
 import typer
 
-from obsidian_metadata._utils import alerts, vault_validation
+from obsidian_metadata._utils import Questions, alerts
 from obsidian_metadata._utils.alerts import logger as log
 
-try:
-    import tomllib
-except ModuleNotFoundError:
-    import tomli as tomllib  # type: ignore [no-redef]
-
-DEFAULT_CONFIG_FILE: Path = Path(__file__).parent / "default.toml"
-
 
 @rich.repr.auto
 class Config:
-    """Configuration class."""
+    """Representation of a configuration file."""
 
     def __init__(self, config_path: Path = None, vault_path: Path = None) -> None:
-        self.config_path: Path = self._validate_config_path(Path(config_path))
-        self.config: dict[str, Any] = self._load_config()
-        self.config_content: str = self.config_path.read_text()
-        self.vault_path: Path = self._validate_vault_path(vault_path)
+
+        if vault_path is None:
+            self.config_path: Path = self._validate_config_path(Path(config_path))
+            self.config: dict[str, Any] = self._load_config()
+
+            if self.config == {}:
+                log.error(f"Configuration file is empty: '{self.config_path}'")
+                raise typer.Exit(code=1)
+        else:
+            self.config_path = None
+            self.config = {
+                "command_line_vault": {"path": vault_path, "exclude_paths": [".git", ".obsidian"]}
+            }
 
         try:
-            self.exclude_paths: list[Any] = self.config["exclude_paths"]
-        except KeyError:
-            self.exclude_paths = []
-
-        try:
-            self.metadata_location: str = self.config["metadata"]["metadata_location"]
-        except KeyError:
-            self.metadata_location = "frontmatter"
-
-        try:
-            self.tags_location: str = self.config["metadata"]["tags_location"]
-        except KeyError:
-            self.tags_location = "top"
+            self.vaults: list[VaultConfig] = [
+                VaultConfig(vault_name=key, vault_config=self.config[key]) for key in self.config
+            ]
+        except TypeError as e:
+            log.error(f"Configuration file is invalid: '{self.config_path}'")
+            raise typer.Exit(code=1) from e
 
         log.debug(f"Loaded configuration from '{self.config_path}'")
         log.trace(self.config)
 
     def __rich_repr__(self) -> rich.repr.Result:  # pragma: no cover
-        """Define rich representation of Vault."""
+        """Define rich representation of the Config object."""
         yield "config_path", self.config_path
-        yield "config_content",
-        yield "vault_path", self.vault_path
-        yield "metadata_location", self.metadata_location
-        yield "tags_location", self.tags_location
-        yield "exclude_paths", self.exclude_paths
+        yield "vaults", self.vaults
 
     def _validate_config_path(self, config_path: Path | None) -> Path:
         """Load the configuration path."""
@@ -63,7 +54,7 @@ class Config:
             config_path = Path(Path.home() / f".{__package__.split('.')[0]}.toml")
 
         if not config_path.exists():
-            shutil.copy(DEFAULT_CONFIG_FILE, config_path)
+            self._write_default_config(config_path)
             alerts.info(f"Created default configuration file at '{config_path}'")
 
         return config_path.expanduser().resolve()
@@ -71,46 +62,67 @@ class Config:
     def _load_config(self) -> dict[str, Any]:
         """Load the configuration file."""
         try:
-            with self.config_path.open("rb") as f:
-                return tomllib.load(f)
-        except tomllib.TOMLDecodeError as e:
+            with open(self.config_path, encoding="utf-8") as fp:
+                return tomlkit.load(fp)
+        except tomlkit.exceptions.TOMLKitError as e:
             alerts.error(f"Could not parse '{self.config_path}'")
             raise typer.Exit(code=1) from e
 
+    def _write_default_config(self, path_to_config: Path) -> None:
+        """Write the default configuration file when no config file is found."""
+        vault_path = Questions.ask_for_vault_path()
+
+        config_text = f"""\
+        # Add another vault by replicating this section and changing the name
+        ["Vault 1"] # Name of the vault.
+
+            # Path to your obsidian vault
+            path = "{vault_path}"
+
+            # Folders within the vault to ignore when indexing metadata
+            exclude_paths = [".git", ".obsidian"]"""
+
+        path_to_config.write_text(dedent(config_text))
+
+
+@rich.repr.auto
+class VaultConfig:
+    """Representation of a vault configuration."""
+
+    def __init__(self, vault_name: str, vault_config: dict) -> None:
+        """Initialize the vault configuration."""
+        self.name: str = vault_name
+        self.config: dict = vault_config
+
+        try:
+            self.path = self._validate_vault_path(self.config["path"])
+
+            Path(self.config["path"]).expanduser().resolve()
+        except KeyError:
+            self.path = None
+
+        try:
+            self.exclude_paths = self.config["exclude_paths"]
+        except KeyError:
+            self.exclude_paths = []
+
+    def __rich_repr__(self) -> rich.repr.Result:  # pragma: no cover
+        """Define rich representation of a vault config."""
+        yield "name", self.name
+        yield "config", self.config
+        yield "path", self.path
+        yield "exclude_paths", self.exclude_paths
+
     def _validate_vault_path(self, vault_path: Path | None) -> Path:
         """Validate the vault path."""
-        if vault_path is None:
-            try:
-                vault_path = Path(self.config["vault"]).expanduser().resolve()
-            except KeyError:
-                vault_path = Path("/I/Do/Not/Exist")
+        vault_path = Path(vault_path).expanduser().resolve()
 
-        if not vault_path.exists():  # pragma: no cover
+        if not vault_path.exists():
             alerts.error(f"Vault path not found: '{vault_path}'")
+            raise typer.Exit(code=1)
 
-            vault_path = questionary.path(
-                "Enter a path to Obsidian vault:",
-                only_directories=True,
-                validate=vault_validation,
-            ).ask()
-            if vault_path is None:
-                raise typer.Exit(code=1)
+        if not vault_path.is_dir():
+            alerts.error(f"Vault path is not a directory: '{vault_path}'")
+            raise typer.Exit(code=1)
 
-            vault_path = Path(vault_path).expanduser().resolve()
-
-            self.write_config_value("vault", str(vault_path))
         return vault_path
-
-    def write_config_value(self, key: str, value: str | int) -> None:
-        """Write a new value to the configuration file.
-
-        Args:
-            key (str): The key to write.
-            value (str|int): The value to write.
-        """
-        self.config_content = re.sub(
-            rf"( *{key} = ['\"])[^'\"]*(['\"].*)", rf"\1{value}\2", self.config_content
-        )
-
-        alerts.notice(f"Writing new configuration for '{key}' to '{self.config_path}'")
-        self.config_path.write_text(self.config_content)
diff --git a/src/obsidian_metadata/_config/default.toml b/src/obsidian_metadata/_config/default.toml
deleted file mode 100644
index a6f94da..0000000
--- a/src/obsidian_metadata/_config/default.toml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Path to your obsidian vault
-vault = "/path/to/vault"
-
-# Folders within the vault to ignore when indexing metadata
-exclude_paths = [".git", ".obsidian"]
diff --git a/src/obsidian_metadata/_utils/__init__.py b/src/obsidian_metadata/_utils/__init__.py
index b00ef24..82b44b7 100644
--- a/src/obsidian_metadata/_utils/__init__.py
+++ b/src/obsidian_metadata/_utils/__init__.py
@@ -2,6 +2,7 @@
 
 from obsidian_metadata._utils import alerts
 from obsidian_metadata._utils.alerts import LoggerManager
+from obsidian_metadata._utils.questions import Questions
 from obsidian_metadata._utils.utilities import (
     clean_dictionary,
     clear_screen,
@@ -9,7 +10,6 @@ from obsidian_metadata._utils.utilities import (
     dict_values_to_lists_strings,
     docstring_parameter,
     remove_markdown_sections,
-    vault_validation,
     version_callback,
 )
 
@@ -21,6 +21,7 @@ __all__ = [
     "dict_contains",
     "docstring_parameter",
     "LoggerManager",
+    "Questions",
     "remove_markdown_sections",
     "vault_validation",
     "version_callback",
diff --git a/src/obsidian_metadata/_utils/questions.py b/src/obsidian_metadata/_utils/questions.py
new file mode 100644
index 0000000..01ad6ee
--- /dev/null
+++ b/src/obsidian_metadata/_utils/questions.py
@@ -0,0 +1,33 @@
+"""Functions for asking questions to the user and validating responses."""
+from pathlib import Path
+
+import questionary
+import typer
+
+
+class Questions:
+    """Class for asking questions to the user and validating responses."""
+
+    @staticmethod
+    def ask_for_vault_path() -> Path:  # pragma: no cover
+        """Ask the user for the path to their vault."""
+        vault_path = questionary.path(
+            "Enter a path to Obsidian vault:",
+            only_directories=True,
+            validate=Questions._validate_vault,
+        ).ask()
+        if vault_path is None:
+            raise typer.Exit(code=1)
+
+        return Path(vault_path).expanduser().resolve()
+
+    @staticmethod
+    def _validate_vault(path: str) -> bool | str:
+        """Validates the vault path."""
+        path_to_validate: Path = Path(path).expanduser().resolve()
+        if not path_to_validate.exists():
+            return f"Path does not exist: {path_to_validate}"
+        if not path_to_validate.is_dir():
+            return f"Path is not a directory: {path_to_validate}"
+
+        return True
diff --git a/src/obsidian_metadata/_utils/utilities.py b/src/obsidian_metadata/_utils/utilities.py
index 8bedcf8..5667355 100644
--- a/src/obsidian_metadata/_utils/utilities.py
+++ b/src/obsidian_metadata/_utils/utilities.py
@@ -1,7 +1,6 @@
 """Utility functions."""
 import re
 from os import name, system
-from pathlib import Path
 from typing import Any
 
 import typer
@@ -83,17 +82,6 @@ def version_callback(value: bool) -> None:
         raise typer.Exit()
 
 
-def vault_validation(path: str) -> bool | str:
-    """Validates the vault path."""
-    path_to_validate: Path = Path(path).expanduser().resolve()
-    if not path_to_validate.exists():
-        return f"Path does not exist: {path_to_validate}"
-    if not path_to_validate.is_dir():
-        return f"Path is not a directory: {path_to_validate}"
-
-    return True
-
-
 def docstring_parameter(*sub: Any) -> Any:
     """Decorator to replace variables within docstrings.
 
diff --git a/src/obsidian_metadata/cli.py b/src/obsidian_metadata/cli.py
index e3cf36f..1d1636b 100644
--- a/src/obsidian_metadata/cli.py
+++ b/src/obsidian_metadata/cli.py
@@ -4,11 +4,17 @@
 from pathlib import Path
 from typing import Optional
 
+import questionary
 import typer
 from rich import print
 
 from obsidian_metadata._config import Config
-from obsidian_metadata._utils import alerts, docstring_parameter, version_callback
+from obsidian_metadata._utils import (
+    alerts,
+    clear_screen,
+    docstring_parameter,
+    version_callback,
+)
 from obsidian_metadata.models import Application
 
 app = typer.Typer(add_completion=False, no_args_is_help=True, rich_markup_mode="rich")
@@ -95,9 +101,6 @@ def main(
         log_to_file,
     )
 
-    config: Config = Config(config_path=config_file, vault_path=vault_path)
-    application = Application(dry_run=dry_run, config=config)
-
     banner = r"""
    ___  _         _     _ _
   / _ \| |__  ___(_) __| (_) __ _ _ __
@@ -109,7 +112,28 @@ def main(
  | |  | |  __/ || (_| | (_| | (_| | || (_| |
  |_|  |_|\___|\__\__,_|\__,_|\__,_|\__\__,_|
 """
+    clear_screen()
     print(banner)
+
+    config: Config = Config(config_path=config_file, vault_path=vault_path)
+    if len(config.vaults) == 0:
+        typer.echo("No vaults configured. Exiting.")
+        raise typer.Exit(1)
+
+    if len(config.vaults) == 1:
+        application = Application(dry_run=dry_run, config=config.vaults[0])
+    else:
+        vault_names = [vault.name for vault in config.vaults]
+        vault_name = questionary.select(
+            "Select a vault to process:",
+            choices=vault_names,
+        ).ask()
+        if vault_name is None:
+            raise typer.Exit(code=1)
+
+        vault_to_use = next(vault for vault in config.vaults if vault.name == vault_name)
+        application = Application(dry_run=dry_run, config=vault_to_use)
+
     application.main_app()
 
 
diff --git a/src/obsidian_metadata/models/application.py b/src/obsidian_metadata/models/application.py
index de25aa0..f2d7c1d 100644
--- a/src/obsidian_metadata/models/application.py
+++ b/src/obsidian_metadata/models/application.py
@@ -6,8 +6,8 @@ from typing import Any
 import questionary
 from rich import print
 
-from obsidian_metadata._config import Config
-from obsidian_metadata._utils import alerts, clear_screen
+from obsidian_metadata._config import VaultConfig
+from obsidian_metadata._utils import alerts
 from obsidian_metadata._utils.alerts import logger as log
 from obsidian_metadata.models import Patterns, Vault
 
@@ -22,7 +22,7 @@ class Application:
     More info: https://questionary.readthedocs.io/en/stable/pages/advanced.html#create-questions-from-dictionaries
     """
 
-    def __init__(self, config: Config, dry_run: bool) -> None:
+    def __init__(self, config: VaultConfig, dry_run: bool) -> None:
         self.config = config
         self.dry_run = dry_run
         self.custom_style = questionary.Style(
@@ -45,7 +45,6 @@ class Application:
 
     def main_app(self) -> None:  # noqa: C901
         """Questions for the main application."""
-        clear_screen()
         self.load_vault()
 
         while True:
diff --git a/src/obsidian_metadata/models/vault.py b/src/obsidian_metadata/models/vault.py
index dbe99bf..1891728 100644
--- a/src/obsidian_metadata/models/vault.py
+++ b/src/obsidian_metadata/models/vault.py
@@ -10,7 +10,7 @@ from rich.progress import Progress, SpinnerColumn, TextColumn
 from rich.prompt import Confirm
 from rich.table import Table
 
-from obsidian_metadata._config import Config
+from obsidian_metadata._config import VaultConfig
 from obsidian_metadata._utils import alerts
 from obsidian_metadata._utils.alerts import logger as log
 from obsidian_metadata.models import Note, VaultMetadata
@@ -27,8 +27,8 @@ class Vault:
         notes (list[Note]): List of all notes in the vault.
     """
 
-    def __init__(self, config: Config, dry_run: bool = False, path_filter: str = None):
-        self.vault_path: Path = config.vault_path
+    def __init__(self, config: VaultConfig, dry_run: bool = False, path_filter: str = None):
+        self.vault_path: Path = config.path
         self.dry_run: bool = dry_run
         self.backup_path: Path = self.vault_path.parent / f"{self.vault_path.name}.bak"
         self.exclude_paths: list[Path] = []
diff --git a/tests/application_test.py b/tests/application_test.py
index 6f528ea..976d43d 100644
--- a/tests/application_test.py
+++ b/tests/application_test.py
@@ -10,9 +10,10 @@ def test_load_vault(test_vault) -> None:
     """Test application."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    app = Application(config=config, dry_run=False)
+    vault_config = config.vaults[0]
+    app = Application(config=vault_config, dry_run=False)
     app.load_vault()
 
     assert app.dry_run is False
-    assert app.config == config
-    assert app.vault.num_notes() == 2
+    assert app.config == vault_config
+    assert app.vault.num_notes() == 3
diff --git a/tests/config_test.py b/tests/config_test.py
index 3873bc6..39dd8b6 100644
--- a/tests/config_test.py
+++ b/tests/config_test.py
@@ -1,28 +1,109 @@
 # type: ignore
 """Tests for the configuration module."""
 
-import re
 from pathlib import Path
+from textwrap import dedent
+
+import pytest
+import typer
 
 from obsidian_metadata._config import Config
 
 
-def test_first_run(tmp_path):
-    """Test creating a config on first run."""
-    config_file = Path(tmp_path / "config.toml")
-    vault_path = Path(tmp_path / "vault/")
-    vault_path.mkdir()
+def test_broken_config_file(capsys) -> None:
+    """Test loading a broken config file."""
+    config_file = Path("tests/fixtures/broken_config_file.toml")
 
-    config = Config(config_path=config_file, vault_path=vault_path)
+    with pytest.raises(typer.Exit):
+        Config(config_path=config_file)
+    captured = capsys.readouterr()
+    assert "Could not parse" in captured.out
+
+
+def test_vault_path_errors(tmp_path, capsys) -> None:
+    """Test loading a config file with a vault path that doesn't exist."""
+    config_file = Path(tmp_path / "config.toml")
+    with pytest.raises(typer.Exit):
+        Config(config_path=config_file, vault_path=Path("tests/fixtures/does_not_exist"))
+    captured = capsys.readouterr()
+    assert "Vault path not found" in captured.out
+
+    with pytest.raises(typer.Exit):
+        Config(config_path=config_file, vault_path=Path("tests/fixtures/sample_note.md"))
+    captured = capsys.readouterr()
+    assert "Vault path is not a directory" in captured.out
+
+
+def test_multiple_vaults_okay() -> None:
+    """Test multiple vaults."""
+    config_file = Path("tests/fixtures/multiple_vaults.toml")
+
+    config = Config(config_path=config_file)
+    assert config.config == {
+        "Sample Vault": {
+            "exclude_paths": [".git", ".obsidian", "ignore_folder"],
+            "path": "tests/fixtures/sample_vault",
+        },
+        "Test Vault": {
+            "exclude_paths": [".git", ".obsidian", "ignore_folder"],
+            "path": "tests/fixtures/test_vault",
+        },
+    }
+    assert len(config.vaults) == 2
+    assert config.vaults[0].name == "Sample Vault"
+    assert config.vaults[0].path == Path("tests/fixtures/sample_vault").expanduser().resolve()
+    assert config.vaults[0].exclude_paths == [".git", ".obsidian", "ignore_folder"]
+    assert config.vaults[1].name == "Test Vault"
+    assert config.vaults[1].path == Path("tests/fixtures/test_vault").expanduser().resolve()
+    assert config.vaults[1].exclude_paths == [".git", ".obsidian", "ignore_folder"]
+
+
+def test_single_vault() -> None:
+    """Test multiple vaults."""
+    config_file = Path("tests/fixtures/test_vault_config.toml")
+
+    config = Config(config_path=config_file)
+    assert config.config == {
+        "Test Vault": {
+            "exclude_paths": [".git", ".obsidian", "ignore_folder"],
+            "path": "tests/fixtures/test_vault",
+        }
+    }
+    assert len(config.vaults) == 1
+    assert config.vaults[0].name == "Test Vault"
+    assert config.vaults[0].path == Path("tests/fixtures/test_vault").expanduser().resolve()
+    assert config.vaults[0].exclude_paths == [".git", ".obsidian", "ignore_folder"]
+
+
+def test_no_config_no_vault(tmp_path, mocker) -> None:
+    """Test creating a config on first run."""
+    fake_vault = Path(tmp_path / "vault")
+    fake_vault.mkdir()
+    mocker.patch(
+        "obsidian_metadata._config.config.Questions.ask_for_vault_path", return_value=fake_vault
+    )
+
+    config_file = Path(tmp_path / "config.toml")
+    Config(config_path=config_file)
+
+    content = config_file.read_text()
+    sample_config = f"""\
+    # Add another vault by replicating this section and changing the name
+    ["Vault 1"] # Name of the vault.
+
+        # Path to your obsidian vault
+        path = "{str(fake_vault)}"
+
+        # Folders within the vault to ignore when indexing metadata
+        exclude_paths = [".git", ".obsidian"]"""
 
     assert config_file.exists() is True
-    config.write_config_value("vault", str(vault_path))
-    content = config_file.read_text()
-    assert config.vault_path == vault_path
-    assert re.search(str(vault_path), content) is not None
+    assert content == dedent(sample_config)
 
-
-def test_parse_config():
-    """Test parsing a config file."""
-    config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=None)
-    assert config.vault_path == Path(Path.cwd() / "tests/fixtures/test_vault")
+    new_config = Config(config_path=config_file)
+    assert new_config.config == {
+        "Vault 1": {
+            "path": str(fake_vault),
+            "exclude_paths": [".git", ".obsidian"],
+        }
+    }
diff --git a/tests/fixtures/broken_config_file.toml b/tests/fixtures/broken_config_file.toml
new file mode 100644
index 0000000..29568cb
--- /dev/null
+++ b/tests/fixtures/broken_config_file.toml
@@ -0,0 +1,6 @@
+["Sample Vault]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/sample_vault"
+["Test Vault"]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/test_vault"
diff --git a/tests/fixtures/multiple_vaults.toml b/tests/fixtures/multiple_vaults.toml
new file mode 100644
index 0000000..034276e
--- /dev/null
+++ b/tests/fixtures/multiple_vaults.toml
@@ -0,0 +1,6 @@
+["Sample Vault"]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/sample_vault"
+["Test Vault"]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/test_vault"
diff --git a/tests/fixtures/sample_vault_config.toml b/tests/fixtures/sample_vault_config.toml
index 208e62f..a904439 100644
--- a/tests/fixtures/sample_vault_config.toml
+++ b/tests/fixtures/sample_vault_config.toml
@@ -1,8 +1,3 @@
-vault = "tests/fixtures/sample_vault"
-
-# folders to ignore when parsing content
-exclude_paths = [".git", ".obsidian", "ignore_folder"]
-
-[metadata]
-    metadata_location = "frontmatter" # "frontmatter", "top", "bottom"
-    tags_location     = "top"         # "frontmatter", "top", "bottom"
+["Sample Vault"]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/sample_vault"
diff --git a/tests/fixtures/test_vault/ignore_folder/file_to_ignore.md b/tests/fixtures/test_vault/ignore_folder/file_to_ignore.md
index 971f792..5aa71d3 100644
--- a/tests/fixtures/test_vault/ignore_folder/file_to_ignore.md
+++ b/tests/fixtures/test_vault/ignore_folder/file_to_ignore.md
@@ -8,6 +8,7 @@ tags:
   - ignored_file_tag1
 author: author name
 type: ["article", "note"]
+ignored_frontmatter: ignore_me
 ---
 #inline_tag_top1 #inline_tag_top2
 #ignored_file_tag2
diff --git a/tests/fixtures/test_vault_config.toml b/tests/fixtures/test_vault_config.toml
index de72145..044336e 100644
--- a/tests/fixtures/test_vault_config.toml
+++ b/tests/fixtures/test_vault_config.toml
@@ -1,8 +1,3 @@
-vault = "tests/fixtures/test_vault"
-
-# folders to ignore when parsing content
-exclude_paths = [".git", ".obsidian", "ignore_folder"]
-
-[metadata]
-    metadata_location = "frontmatter" # "frontmatter", "top", "bottom"
-    tags_location     = "top"         # "frontmatter", "top", "bottom"
+["Test Vault"]
+    exclude_paths = [".git", ".obsidian", "ignore_folder"]
+    path          = "tests/fixtures/test_vault"
diff --git a/tests/questions_test.py b/tests/questions_test.py
new file mode 100644
index 0000000..71b4ace
--- /dev/null
+++ b/tests/questions_test.py
@@ -0,0 +1,12 @@
+# type: ignore
+"""Test the questions class."""
+
+
+from obsidian_metadata._utils import Questions
+
+
+def test_vault_validation():
+    """Test vault validation."""
+    assert Questions._validate_vault("tests/") is True
+    assert "Path is not a directory" in Questions._validate_vault("pyproject.toml")
+    assert "Path does not exist" in Questions._validate_vault("tests/vault2")
diff --git a/tests/utilities_test.py b/tests/utilities_test.py
index 2ea83ed..d487c0f 100644
--- a/tests/utilities_test.py
+++ b/tests/utilities_test.py
@@ -7,7 +7,6 @@ from obsidian_metadata._utils import (
     dict_contains,
     dict_values_to_lists_strings,
     remove_markdown_sections,
-    vault_validation,
 )
 
 
@@ -67,13 +66,6 @@ def test_dict_values_to_lists_strings():
     }
 
 
-def test_vault_validation():
-    """Test vault validation."""
-    assert vault_validation("tests/") is True
-    assert "Path is not a directory" in vault_validation("pyproject.toml")
-    assert "Path does not exist" in vault_validation("tests/vault2")
-
-
 def test_remove_markdown_sections():
     """Test removing markdown sections."""
     text: str = """
diff --git a/tests/vault_test.py b/tests/vault_test.py
index 461a0a4..226fd7e 100644
--- a/tests/vault_test.py
+++ b/tests/vault_test.py
@@ -12,16 +12,18 @@ def test_vault_creation(test_vault):
     """Test creating a Vault object."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.vault_path == vault_path
     assert vault.backup_path == Path(f"{vault_path}.bak")
     assert vault.dry_run is False
     assert str(vault.exclude_paths[0]) == Regex(r".*\.git")
-    assert vault.num_notes() == 2
+    assert vault.num_notes() == 3
 
     assert vault.metadata.dict == {
         "Inline Tags": [
+            "ignored_file_tag2",
             "inline_tag_bottom1",
             "inline_tag_bottom2",
             "inline_tag_top1",
@@ -30,24 +32,29 @@ def test_vault_creation(test_vault):
             "intext_tag2",
             "shared_tag",
         ],
+        "author": ["author name"],
         "bottom_key1": ["bottom_key1_value"],
         "bottom_key2": ["bottom_key2_value"],
         "date_created": ["2022-12-22"],
         "emoji_📅_key": ["emoji_📅_key_value"],
         "frontmatter_Key1": ["author name"],
         "frontmatter_Key2": ["article", "note"],
+        "ignored_frontmatter": ["ignore_me"],
         "intext_key": ["intext_value"],
         "shared_key1": ["shared_key1_value"],
         "shared_key2": ["shared_key2_value1", "shared_key2_value2"],
         "tags": [
             "frontmatter_tag1",
             "frontmatter_tag2",
+            "frontmatter_tag3",
+            "ignored_file_tag1",
             "shared_tag",
             "📅/frontmatter_tag3",
         ],
         "top_key1": ["top_key1_value"],
         "top_key2": ["top_key2_value"],
         "top_key3": ["top_key3_value_as_link"],
+        "type": ["article", "note"],
     }
 
 
@@ -55,13 +62,15 @@ def test_get_filtered_notes(sample_vault) -> None:
     """Test filtering notes."""
     vault_path = sample_vault
     config = Config(config_path="tests/fixtures/sample_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config, path_filter="front")
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config, path_filter="front")
 
     assert vault.num_notes() == 4
 
     vault_path = sample_vault
     config = Config(config_path="tests/fixtures/sample_vault_config.toml", vault_path=vault_path)
-    vault2 = Vault(config=config, path_filter="mixed")
+    vault_config = config.vaults[0]
+    vault2 = Vault(config=vault_config, path_filter="mixed")
 
     assert vault2.num_notes() == 1
 
@@ -70,7 +79,8 @@ def test_backup(test_vault, capsys):
     """Test backing up the vault."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config, dry_run=False)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     vault.backup()
 
@@ -88,7 +98,8 @@ def test_backup_dryrun(test_vault, capsys):
     """Test backing up the vault."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config, dry_run=True)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config, dry_run=True)
 
     print(f"vault.dry_run: {vault.dry_run}")
     vault.backup()
@@ -102,7 +113,8 @@ def test_delete_backup(test_vault, capsys):
     """Test deleting the vault backup."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config, dry_run=False)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     vault.backup()
     vault.delete_backup()
@@ -121,7 +133,8 @@ def test_delete_backup_dryrun(test_vault, capsys):
     """Test deleting the vault backup."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config, dry_run=True)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config, dry_run=True)
 
     Path.mkdir(vault.backup_path)
     vault.delete_backup()
@@ -135,7 +148,8 @@ def test_info(test_vault, capsys):
     """Test printing vault information."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     vault.info()
 
@@ -149,7 +163,8 @@ def test_contains_inline_tag(test_vault) -> None:
     """Test if the vault contains an inline tag."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.contains_inline_tag("tag") is False
     assert vault.contains_inline_tag("intext_tag2") is True
@@ -159,7 +174,8 @@ def test_contains_metadata(test_vault) -> None:
     """Test if the vault contains a metadata key."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.contains_metadata("key") is False
     assert vault.contains_metadata("top_key1") is True
@@ -171,11 +187,13 @@ def test_delete_inline_tag(test_vault) -> None:
     """Test deleting an inline tag."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.delete_inline_tag("no tag") is False
     assert vault.delete_inline_tag("intext_tag2") is True
     assert vault.metadata.dict["Inline Tags"] == [
+        "ignored_file_tag2",
         "inline_tag_bottom1",
         "inline_tag_bottom2",
         "inline_tag_top1",
@@ -189,15 +207,16 @@ def test_delete_metadata(test_vault) -> None:
     """Test deleting a metadata key/value."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.delete_metadata("no key") == 0
     assert vault.delete_metadata("top_key1", "no_value") == 0
 
-    assert vault.delete_metadata("top_key1", "top_key1_value") == 1
+    assert vault.delete_metadata("top_key1", "top_key1_value") == 2
     assert vault.metadata.dict["top_key1"] == []
 
-    assert vault.delete_metadata("top_key2") == 1
+    assert vault.delete_metadata("top_key2") == 2
     assert "top_key2" not in vault.metadata.dict
 
 
@@ -205,11 +224,13 @@ def test_rename_inline_tag(test_vault) -> None:
     """Test renaming an inline tag."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.rename_inline_tag("no tag", "new_tag") is False
     assert vault.rename_inline_tag("intext_tag2", "new_tag") is True
     assert vault.metadata.dict["Inline Tags"] == [
+        "ignored_file_tag2",
         "inline_tag_bottom1",
         "inline_tag_bottom2",
         "inline_tag_top1",
@@ -224,7 +245,8 @@ def test_rename_metadata(test_vault) -> None:
     """Test renaming a metadata key/value."""
     vault_path = test_vault
     config = Config(config_path="tests/fixtures/test_vault_config.toml", vault_path=vault_path)
-    vault = Vault(config=config)
+    vault_config = config.vaults[0]
+    vault = Vault(config=vault_config)
 
     assert vault.rename_metadata("no key", "new_key") is False
     assert vault.rename_metadata("tags", "nonexistent_value", "new_vaule") is False
@@ -232,6 +254,8 @@ def test_rename_metadata(test_vault) -> None:
     assert vault.rename_metadata("tags", "frontmatter_tag1", "new_vaule") is True
     assert vault.metadata.dict["tags"] == [
         "frontmatter_tag2",
+        "frontmatter_tag3",
+        "ignored_file_tag1",
         "new_vaule",
         "shared_tag",
         "📅/frontmatter_tag3",
@@ -241,6 +265,8 @@ def test_rename_metadata(test_vault) -> None:
     assert "tags" not in vault.metadata.dict
     assert vault.metadata.dict["new_key"] == [
         "frontmatter_tag2",
+        "frontmatter_tag3",
+        "ignored_file_tag1",
         "new_vaule",
         "shared_tag",
         "📅/frontmatter_tag3",