diff --git a/docs/pages/config.rst b/docs/pages/config.rst
index f8868e0..4ed3ab6 100644
--- a/docs/pages/config.rst
+++ b/docs/pages/config.rst
@@ -39,3 +39,6 @@ Substitute ``tool`` for either ``format``, ``xml_sort``, ``git_info`` or ``make_
 
 See pages about each tool for available options.
 The options are named the same as the command line arguments, except without any leading dashes and with any other dashes (``-``) replaced by underscores (``_``).
+
+Note that when a filepath is being used, it is considered relative to the config file it's in.
+This is different from when using the option from a commandline, where the current working directory is used as a root.
diff --git a/src/tctools/common.py b/src/tctools/common.py
index 8cfe264..20dff20 100644
--- a/src/tctools/common.py
+++ b/src/tctools/common.py
@@ -30,6 +30,8 @@ class Tool(ABC):
 
     CONFIG_KEY: Optional[str] = None
 
+    PATH_VARIABLES: List[str] = []  # Names of options that are considered file paths
+
     def __init__(self, *args):
         """Pass e.g. ``sys.args[1:]`` (skipping the script part of the arguments).
 
@@ -54,6 +56,11 @@ def __init__(self, *args):
                 raise ValueError(
                     f"Config field `{key}` is not recognized as a valid option"
                 )
+            if key in self.PATH_VARIABLES:
+                value = self._make_path_from_config(value)
+                # We should treat these paths as relative to the config file, ignoring
+                # the current working directory
+
             parser.set_defaults(**{key: value})
 
             for action in parser._actions:
@@ -128,6 +135,27 @@ def _find_files_upwards(
 
         return None
 
+    def _make_path_from_config(self, path: Any) -> Path:
+        """Turn a relative path from a config file into a global path.
+
+        Otherwise, return it as-is.
+
+        :param path: Config value, can be (list of) `Path` or `str`
+        """
+
+        def _fix_path(p):
+            p = Path(p)
+            if not p.is_absolute() and self.config_file:
+                p = self.config_file.parent / p
+            return p
+
+        if isinstance(path, list):
+            path = [_fix_path(p) for p in path]
+        else:
+            path = _fix_path(path)
+
+        return path
+
     @abstractmethod
     def run(self) -> int:
         """Main tool execution."""
@@ -146,6 +174,8 @@ def get_logger(self):
 class TcTool(Tool, ABC):
     """Base class for tools sharing TwinCAT functionality."""
 
+    PATH_VARIABLES = ["target"]
+
     def __init__(self, *args):
         super().__init__(*args)
 
@@ -217,7 +247,7 @@ def find_files(self) -> List[Path]:
             return files
 
         targets = self.args.target
-        if isinstance(targets, str):
+        if isinstance(targets, str) or isinstance(targets, Path):
             targets = [targets]
 
         for target in targets:
diff --git a/tests/test_common.py b/tests/test_common.py
index dc6170a..244e751 100644
--- a/tests/test_common.py
+++ b/tests/test_common.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import pytest  # noqa
 
 from tctools.common import Tool
@@ -8,6 +10,8 @@ class MyTool(Tool):
 
     CONFIG_KEY = "dummy"
 
+    PATH_VARIABLES = ["my_file", "my_targets"]
+
     @classmethod
     def set_arguments(cls, parser):
         super().set_arguments(parser)
@@ -17,6 +21,16 @@ def set_arguments(cls, parser):
             action="store",
             default="default-text",
         )
+        parser.add_argument(
+            "--my-file",
+            action="store",
+            default="default-text",
+        )
+        parser.add_argument(
+            "--my-targets",
+            action="store",
+            default="default-text",
+        )
         return parser
 
     def run(self) -> int:
@@ -73,3 +87,29 @@ def test_config_file_priority(self, tmp_path, monkeypatch):
 
         tool = MyTool()
         assert tool.args.my_option == "abc987"
+
+    def test_config_file_relative_path(self, tmp_path, monkeypatch):
+        conf_dir = tmp_path / "project"
+        work_dir = conf_dir / "subdir1" / "subdir2"
+        work_dir.mkdir(parents=True)
+
+        conf_file = conf_dir / "tctools.toml"
+        conf_file.write_text(
+            """[tctools.dummy]
+    my_file = "some_file.txt"
+    my_targets = ["./dir1", "dir2/subdir2/", "//abs_dir/absolute_file.txt"]
+    """
+        )
+
+        monkeypatch.chdir(work_dir)  # Run in child dir of config file dir
+
+        tool = MyTool()
+        assert not tool.args.my_file.is_relative_to(work_dir)
+        assert tool.args.my_file == conf_dir / "some_file.txt"
+
+        assert not tool.args.my_targets[0].is_relative_to(work_dir)
+        assert not tool.args.my_targets[1].is_relative_to(work_dir)
+        assert not tool.args.my_targets[2].is_relative_to(work_dir)
+        assert tool.args.my_targets[0] == conf_dir / "dir1"
+        assert tool.args.my_targets[1] == conf_dir / "dir2" / "subdir2"
+        assert tool.args.my_targets[2] == Path("//abs_dir/absolute_file.txt")