diff --git a/cmd/bootstrap.go b/cmd/bootstrap.go
index 8f36761..7cba1e4 100644
--- a/cmd/bootstrap.go
+++ b/cmd/bootstrap.go
@@ -121,8 +121,16 @@ func runBootstrap(cmd *cobra.Command, args []string) error {
 			return err
 		}
 		manager := forgejo.NewRepoManager(cfg.Git.BaseURL, cfg.Git.Token, cfg.Git.Owner, cfg.Git.Username, "", "", cfg.Flux.Branch, "")
-		if err := manager.MergePullRequest(cfg.Flux.RepoName, "maidn/bootstrap-"+cfg.ClusterID); err != nil {
-			return err
+		for _, repository := range []string{cfg.Flux.ManifestsRepo, cfg.Flux.RepoName} {
+			open, err := manager.HasOpenPullRequest(repository, "maidn/bootstrap-"+cfg.ClusterID)
+			if err != nil {
+				return err
+			}
+			if open {
+				if err := manager.MergePullRequest(repository, "maidn/bootstrap-"+cfg.ClusterID); err != nil {
+					return err
+				}
+			}
 		}
 	}
 	if bootstrapConfigPath != "" {
diff --git a/internal/bootstrap/bootstrap.go b/internal/bootstrap/bootstrap.go
index 3b4f129..02d7882 100644
--- a/internal/bootstrap/bootstrap.go
+++ b/internal/bootstrap/bootstrap.go
@@ -343,14 +343,16 @@ func (r Runner) Run() error {
 }
 
 func (r Runner) reconcileBootstrapMigration(manager *forgejo.RepoManager) error {
-	if !manager.MigrationPending {
+	if len(manager.MigrationRepositories) == 0 {
 		return nil
 	}
 	if !r.AutoMergeBootstrapMigration {
-		return errors.New("existing repository migration PR created; merge and rerun bootstrap before infrastructure changes")
+		return fmt.Errorf("repository migration PRs created for %s; merge and rerun bootstrap before infrastructure changes", strings.Join(manager.MigrationRepositories, ", "))
 	}
-	if err := manager.MergePullRequest(r.Config.Flux.RepoName, manager.MigrationBranch); err != nil {
-		return fmt.Errorf("merge bootstrap migration PR: %w", err)
+	for _, repository := range manager.MigrationRepositories {
+		if err := manager.MergePullRequest(repository, manager.MigrationBranch); err != nil {
+			return fmt.Errorf("merge bootstrap migration PR for %s: %w", repository, err)
+		}
 	}
 	return nil
 }
diff --git a/internal/bootstrap/bootstrap_test.go b/internal/bootstrap/bootstrap_test.go
index 2f3a50c..ff227f9 100644
--- a/internal/bootstrap/bootstrap_test.go
+++ b/internal/bootstrap/bootstrap_test.go
@@ -908,15 +908,16 @@ func TestRunnerEnableDeliveryAppliesDefaults(t *testing.T) {
 
 func TestRunnerAutoMergesBootstrapMigration(t *testing.T) {
 	server := httptest.NewServer(http.HandlerFunc(func(writer http.ResponseWriter, request *http.Request) {
-		switch request.Method + " " + request.URL.Path {
-		case http.MethodGet + " /api/v1/repos/test-org/cluster/pulls":
+		if request.Method == http.MethodGet && (request.URL.Path == "/api/v1/repos/test-org/manifests/pulls" || request.URL.Path == "/api/v1/repos/test-org/cluster/pulls") {
 			if request.URL.Query().Get("state") != "open" || request.URL.Query().Get("head") != "maidn/bootstrap-test-cluster" {
 				t.Fatalf("unexpected migration lookup query: %q", request.URL.RawQuery)
 			}
 			_ = json.NewEncoder(writer).Encode([]struct {
 				Number int `json:"number"`
 			}{{Number: 4}})
-		case http.MethodPost + " /api/v1/repos/test-org/cluster/pulls/4/merge":
+			return
+		}
+		if request.Method == http.MethodPost && (request.URL.Path == "/api/v1/repos/test-org/manifests/pulls/4/merge" || request.URL.Path == "/api/v1/repos/test-org/cluster/pulls/4/merge") {
 			var body struct {
 				Do string `json:"Do"`
 			}
@@ -924,15 +925,15 @@ func TestRunnerAutoMergesBootstrapMigration(t *testing.T) {
 				t.Fatalf("unexpected migration merge request: %#v, %v", body, err)
 			}
 			writer.WriteHeader(http.StatusOK)
-		default:
-			t.Fatalf("unexpected Forgejo request %s %s", request.Method, request.URL.Path)
+			return
 		}
+		t.Fatalf("unexpected Forgejo request %s %s", request.Method, request.URL.Path)
 	}))
 	defer server.Close()
 
 	manager := forgejo.NewRepoManager(server.URL, "test-token", "test-org", "bot", "manifests", "cluster", "main", "maidn/bootstrap-test-cluster")
 	manager.HTTPClient = server.Client()
-	manager.MigrationPending = true
+	manager.MigrationRepositories = []string{"manifests", "cluster"}
 	if err := (Runner{Config: config.Config{Flux: config.FluxConfig{RepoName: "cluster"}}, AutoMergeBootstrapMigration: true}).reconcileBootstrapMigration(manager); err != nil {
 		t.Fatal(err)
 	}
@@ -946,7 +947,7 @@ func TestRunnerRetainsMigrationApprovalGate(t *testing.T) {
 
 	manager := forgejo.NewRepoManager(server.URL, "test-token", "test-org", "bot", "manifests", "cluster", "main", "maidn/bootstrap-test-cluster")
 	manager.HTTPClient = server.Client()
-	manager.MigrationPending = true
+	manager.MigrationRepositories = []string{"manifests"}
 	if err := (Runner{Config: config.Config{Flux: config.FluxConfig{RepoName: "cluster"}}}).reconcileBootstrapMigration(manager); err == nil || !strings.Contains(err.Error(), "merge and rerun bootstrap") {
 		t.Fatalf("normal bootstrap migration gate = %v", err)
 	}
diff --git a/internal/forgejo/repo.go b/internal/forgejo/repo.go
index dde234e..df2a3a3 100644
--- a/internal/forgejo/repo.go
+++ b/internal/forgejo/repo.go
@@ -16,16 +16,16 @@ import (
 )
 
 type RepoManager struct {
-	BaseURL           string
-	Token             string
-	Owner             string
-	Username          string
-	ManifestsRepoName string
-	FluxRepoName      string
-	Branch            string
-	MigrationBranch   string
-	MigrationPending  bool
-	HTTPClient        *http.Client
+	BaseURL               string
+	Token                 string
+	Owner                 string
+	Username              string
+	ManifestsRepoName     string
+	FluxRepoName          string
+	Branch                string
+	MigrationBranch       string
+	MigrationRepositories []string
+	HTTPClient            *http.Client
 }
 
 type createRepoRequest struct {
@@ -379,7 +379,12 @@ func (rm *RepoManager) setupRepository(repoURL, repoName string, existing bool,
 	if err != nil || !changed || !existing {
 		return err
 	}
-	rm.MigrationPending = true
+	for _, repository := range rm.MigrationRepositories {
+		if repository == repoName {
+			return rm.createMigrationPullRequest(repoName, targetBranch)
+		}
+	}
+	rm.MigrationRepositories = append(rm.MigrationRepositories, repoName)
 	return rm.createMigrationPullRequest(repoName, targetBranch)
 }