diff --git a/src/git/src/mcp_server_git/server.py b/src/git/src/mcp_server_git/server.py
index 5ce953e545..7f2305ffac 100644
--- a/src/git/src/mcp_server_git/server.py
+++ b/src/git/src/mcp_server_git/server.py
@@ -255,6 +255,26 @@ def validate_repo_path(repo_path: Path, allowed_repository: Path | None) -> None
         )
 
 
+def validate_repo_path_against_allowed_repositories(
+    repo_path: Path, allowed_repositories: Sequence[Path]
+) -> None:
+    """Validate that repo_path is within at least one allowed repository path."""
+    if not allowed_repositories:
+        raise ValueError("Repository path is not within the current allowed roots")
+
+    for allowed_repository in allowed_repositories:
+        try:
+            validate_repo_path(repo_path, allowed_repository)
+            return
+        except ValueError:
+            continue
+
+    allowed_list = ", ".join(str(path) for path in allowed_repositories)
+    raise ValueError(
+        f"Repository path '{repo_path}' is outside the allowed repositories: {allowed_list}"
+    )
+
+
 def git_branch(repo: git.Repo, branch_type: str, contains: str | None = None, not_contains: str | None = None) -> str:
     # Defense in depth: reject values starting with '-' to prevent flag injection
     if contains and contains.startswith("-"):
@@ -472,9 +492,17 @@ def by_commandline() -> Sequence[str]:
     @server.call_tool()
     async def call_tool(name: str, arguments: dict) -> list[TextContent]:
         repo_path = Path(arguments["repo_path"])
+        allowed_repositories: list[Path] = []
+        if repository is not None:
+            allowed_repositories.append(repository)
+        allowed_repositories.extend(Path(path) for path in await by_roots())
 
-        # Validate repo_path is within allowed repository
-        validate_repo_path(repo_path, repository)
+        if allowed_repositories:
+            validate_repo_path_against_allowed_repositories(repo_path, allowed_repositories)
+        else:
+            # Preserve the legacy unrestricted behavior when no command-line
+            # repository restriction or root-derived allowlist is available.
+            validate_repo_path(repo_path, repository)
 
         # For all commands, we need an existing repo
         repo = git.Repo(repo_path)
diff --git a/src/git/tests/test_server.py b/src/git/tests/test_server.py
index a5492adc85..857069eb62 100644
--- a/src/git/tests/test_server.py
+++ b/src/git/tests/test_server.py
@@ -16,6 +16,7 @@
     git_create_branch,
     git_show,
     validate_repo_path,
+    validate_repo_path_against_allowed_repositories,
 )
 import shutil
 
@@ -313,6 +314,38 @@ def test_validate_repo_path_symlink_escape(tmp_path: Path):
     with pytest.raises(ValueError) as exc_info:
         validate_repo_path(symlink, allowed)
     assert "outside the allowed repository" in str(exc_info.value)
+
+
+def test_validate_repo_path_against_allowed_repositories_exact_match(tmp_path: Path):
+    allowed_a = tmp_path / "allowed_a"
+    allowed_b = tmp_path / "allowed_b"
+    allowed_a.mkdir()
+    allowed_b.mkdir()
+
+    validate_repo_path_against_allowed_repositories(allowed_b, [allowed_a, allowed_b])
+
+
+def test_validate_repo_path_against_allowed_repositories_rejects_removed_root(tmp_path: Path):
+    allowed_a = tmp_path / "allowed_a"
+    allowed_b = tmp_path / "allowed_b"
+    stale_repo = allowed_a / "repo"
+    allowed_a.mkdir()
+    allowed_b.mkdir()
+    stale_repo.mkdir()
+
+    with pytest.raises(ValueError) as exc_info:
+        validate_repo_path_against_allowed_repositories(stale_repo, [allowed_b])
+    assert "outside the allowed repositories" in str(exc_info.value)
+
+
+def test_validate_repo_path_against_allowed_repositories_rejects_empty_roots(tmp_path: Path):
+    repo = tmp_path / "repo"
+    repo.mkdir()
+
+    with pytest.raises(ValueError) as exc_info:
+        validate_repo_path_against_allowed_repositories(repo, [])
+    assert "current allowed roots" in str(exc_info.value)
+
 # Tests for argument injection protection
 
 def test_git_diff_rejects_flag_injection(test_repository):