diff --git a/lisa/_git.py b/lisa/_git.py
index a22ca3892314b6deb93ddac3ea02dd039e484464..c5afdddd2570807c4851e0ac3c3c85497fdf9a15 100644
--- a/lisa/_git.py
+++ b/lisa/_git.py
@@ -29,8 +29,12 @@ def git(repo, *args):
         # Avoid storing UID/GID in the index. Otherwise, we end up invalidating
         # the entire index when running under a user namespace where the
         # current user got remapped on root.
-         '-c', 'core.checkStat=minimal',
-        '-C', repo,
+        '-c', 'core.checkStat=minimal',
+        # It is critical to use an absolute path here, as path operation in git
+        # seem to be lexical based on that root. By using a resolved path, we
+        # ensure that there is an easy-to-get canonical form for such
+        # parameters.
+        '-C', str(Path(repo).resolve()),
         *args
     )).decode(errors='backslashreplace')
 
@@ -68,15 +72,19 @@ def get_sha1(repo, ref='HEAD'):
     """
     return git(repo, 'rev-list', '-1', ref).strip()
 
-def get_uncommited_patch(repo, include_binary=True):
+def get_uncommited_patch(repo, include_binary=True, path=None):
     """
     Return the patch of non commited changes, both staged and not staged yet.
 
     :param include_binary: If ``True``, include the diff for binary files.
     :type include_binary: bool
+
+    :param path: Path to consider, rather than the entire repo.
+    :type path: str or pathlib.Path
     """
     text = ['--text'] if include_binary else []
-    return git(repo, 'diff', *text, 'HEAD')
+    path = ['--', str(Path(path).resolve())] if path else []
+    return git(repo, 'diff', *text, 'HEAD', *path)
 
 def get_commit_message(repo, ref='HEAD', notes_ref='refs/notes/commits', format='%s'):
     """
diff --git a/lisa/version.py b/lisa/version.py
index 2bd332303bd95d10fbbdda09df58ef87341c38cb..1bcd857668a9e843de832a5c03e5517ebfeec450 100644
--- a/lisa/version.py
+++ b/lisa/version.py
@@ -41,7 +41,9 @@ def _compute_version_token():
 
         try:
             sha1 = get_sha1(repo)
-            patch = get_uncommited_patch(repo)
+            # Get uncommitted content of the LISA sources only, not the entire
+            # repo as it would include things like target_conf.yml
+            patch = get_uncommited_patch(repo, path='lisa/')
         # Git is not installed, just use the regular version
         except (FileNotFoundError, CalledProcessError):
             return plain_version_token