diff --git a/gitindex/index.go b/gitindex/index.go
index 231c6b2c5..7b78bba8b 100644
--- a/gitindex/index.go
+++ b/gitindex/index.go
@@ -236,19 +236,44 @@ func setTemplatesFromConfig(desc *zoekt.Repository, repoDir string) error {
 }
 
 func setTemplatesFromRepo(desc *zoekt.Repository, repo *git.Repository, repoDir string) error {
-	// A caller-supplied name identifies the repository and its shards, so it
-	// takes precedence over names derived from zoekt config or the origin URL.
-	// Other repository fields are intentionally refreshed from that config.
-	if desc.Name != "" {
-		defer func(name string) { desc.Name = name }(desc.Name)
-	}
+	// The caller-supplied name is a fallback for repos without zoekt.name. It
+	// still identifies the repository and shard names better than an inferred
+	// origin URL, but an explicit repo config should win.
+	name := desc.Name
 
 	cfg, err := repo.Config()
 	if err == nil {
-		return setTemplatesFromRepoConfig(desc, cfg)
+		return setTemplatesFromRepoConfigPreservingName(desc, cfg, name)
+	}
+
+	// Some repositories, notably worktrees with .git files, need the plainOpenRepo
+	// fallback to resolve their common dir before go-git can read config.
+	repo, err = plainOpenRepo(repoDir)
+	if err != nil {
+		return err
 	}
 
-	return setTemplatesFromConfig(desc, repoDir)
+	cfg, err = repo.Config()
+	if err != nil {
+		return err
+	}
+
+	return setTemplatesFromRepoConfigPreservingName(desc, cfg, name)
+}
+
+func setTemplatesFromRepoConfigPreservingName(desc *zoekt.Repository, cfg *config.Config, name string) error {
+	if name != "" && cfg.Raw.Section("zoekt").Options.Get("name") == "" {
+		defer func() {
+			// A caller-supplied name identifies the repository and its shards, so it
+			// takes precedence over names derived from the origin URL. Other repository
+			// fields are intentionally refreshed from config.
+			desc.Name = name
+		}()
+	}
+	if err := setTemplatesFromRepoConfig(desc, cfg); err != nil {
+		return err
+	}
+	return nil
 }
 
 func setTemplatesFromRepoConfig(desc *zoekt.Repository, cfg *config.Config) error {
diff --git a/gitindex/index_test.go b/gitindex/index_test.go
index 2b3b54359..133a80482 100644
--- a/gitindex/index_test.go
+++ b/gitindex/index_test.go
@@ -207,6 +207,83 @@ func TestIndexGitRepoPreservesRepositoryName(t *testing.T) {
 	}
 }
 
+func TestIndexGitRepoPrefersConfiguredRepositoryName(t *testing.T) {
+	t.Parallel()
+
+	configuredName := "github.com/sgtest/go-diff"
+	fallbackName := url.QueryEscape(configuredName)
+	repoDir, _ := initGitWorktree(t, "file1.go", "package main\n\nfunc main() {}\n")
+	runGit(t, repoDir, "config", "zoekt.name", configuredName)
+
+	indexDir := t.TempDir()
+	opts := Options{
+		RepoDir:  repoDir,
+		Branches: []string{"HEAD"},
+		BuildOptions: index.Options{
+			RepositoryDescription: zoekt.Repository{Name: fallbackName},
+			IndexDir:              indexDir,
+			DisableCTags:          true,
+		},
+	}
+
+	if _, err := IndexGitRepo(opts); err != nil {
+		t.Fatal(err)
+	}
+	shards, err := filepath.Glob(filepath.Join(indexDir, "*.zoekt"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(shards) != 1 {
+		t.Fatalf("got %d shards, want 1", len(shards))
+	}
+	repositories, _, err := index.ReadMetadataPath(shards[0])
+	if err != nil {
+		t.Fatal(err)
+	}
+	if got := repositories[0].Name; got != configuredName {
+		t.Fatalf("repository name is %q, want %q", got, configuredName)
+	}
+	if got, wantPrefix := filepath.Base(shards[0]), url.QueryEscape(configuredName)+"_v"; !strings.HasPrefix(got, wantPrefix) {
+		t.Fatalf("shard name is %q, want prefix %q", got, wantPrefix)
+	}
+}
+
+func TestIndexGitRepoPreservesRepositoryNameOnTemplateError(t *testing.T) {
+	t.Parallel()
+
+	repoDir, _ := initGitWorktree(t, "file1.go", "package main\n\nfunc main() {}\n")
+	runGit(t, repoDir, "config", "remote.origin.url", "git@example.com:sourcegraph/zoekt.git")
+
+	indexDir := t.TempDir()
+	opts := Options{
+		RepoDir:  repoDir,
+		Branches: []string{"HEAD"},
+		BuildOptions: index.Options{
+			RepositoryDescription: zoekt.Repository{Name: "local/repo"},
+			IndexDir:              indexDir,
+			DisableCTags:          true,
+		},
+	}
+
+	if _, err := IndexGitRepo(opts); err != nil {
+		t.Fatal(err)
+	}
+	shards, err := filepath.Glob(filepath.Join(indexDir, "*.zoekt"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(shards) != 1 {
+		t.Fatalf("got %d shards, want 1", len(shards))
+	}
+	repositories, _, err := index.ReadMetadataPath(shards[0])
+	if err != nil {
+		t.Fatal(err)
+	}
+	if got, want := repositories[0].Name, opts.BuildOptions.RepositoryDescription.Name; got != want {
+		t.Fatalf("repository name is %q, want %q", got, want)
+	}
+}
+
 func TestOpenRepoVariants(t *testing.T) {
 	t.Parallel()