diff --git a/cmd/gazelle/fix-update.go b/cmd/gazelle/fix-update.go
index 44900bf..6a0ffae 100644
--- a/cmd/gazelle/fix-update.go
+++ b/cmd/gazelle/fix-update.go
@@ -238,6 +238,10 @@
 			return nil, fmt.Errorf("-repo_root not specified, and WORKSPACE cannot be found: %v", err)
 		}
 	}
+	uc.c.RepoRoot, err = filepath.EvalSymlinks(uc.c.RepoRoot)
+	if err != nil {
+		return nil, fmt.Errorf("failed to evaluate symlinks for repo root: %v", err)
+	}
 
 	for _, dir := range uc.c.Dirs {
 		if !isDescendingDir(dir, uc.c.RepoRoot) {
diff --git a/internal/config/config.go b/internal/config/config.go
index e5269da..1015d45 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -27,7 +27,8 @@
 	// Dirs is a list of absolute paths to directories where Gazelle should run.
 	Dirs []string
 
-	// RepoRoot is the absolute path to the root directory of the repository.
+	// RepoRoot is the absolute, canonical path to the root directory of the
+	// repository with all symlinks resolved.
 	RepoRoot string
 
 	// ValidBuildFileNames is a list of base names that are considered valid