diff --git a/go.mod b/go.mod
index f353f5e97b..621741c74d 100644
--- a/go.mod
+++ b/go.mod
@@ -19,6 +19,7 @@ require (
 	github.com/ghodss/yaml v1.0.0
 	github.com/go-logr/logr v1.2.3
 	github.com/gogo/protobuf v1.3.2
+	github.com/golang/protobuf v1.5.2
 	github.com/google/go-cmp v0.5.8
 	github.com/google/uuid v1.3.0
 	github.com/google/wire v0.5.0
@@ -143,7 +144,6 @@ require (
 	github.com/gogo/googleapis v1.4.0 // indirect
 	github.com/golang-jwt/jwt/v4 v4.0.0 // indirect
 	github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect
-	github.com/golang/protobuf v1.5.2 // indirect
 	github.com/google/btree v1.0.1 // indirect
 	github.com/google/gofuzz v1.2.0 // indirect
 	github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510 // indirect
diff --git a/internal/tiltfile/tiltextension/plugin_test.go b/internal/tiltfile/tiltextension/plugin_test.go
index 2b1851265b..e5bd69a414 100644
--- a/internal/tiltfile/tiltextension/plugin_test.go
+++ b/internal/tiltfile/tiltextension/plugin_test.go
@@ -163,6 +163,34 @@ printFoo()
 	f.assertLoadRecorded(res, "my-extension")
 }
 
+func TestLoadedExtensionTwiceDifferentFiles(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		// We don't want to have to bother with file:// escaping on windows.
+		// The repo reconciler already tests this.
+		t.Skip()
+	}
+
+	f := newExtensionFixture(t)
+
+	f.tmp.WriteFile(filepath.Join("my-custom-repo", "my-custom-path", "Tiltfile"), libText)
+
+	subfileContent := fmt.Sprintf(`
+v1alpha1.extension_repo(name='my-extension-repo', url='file://%s/my-custom-repo')
+v1alpha1.extension(name='my-extension', repo_name='my-extension-repo', repo_path='my-custom-path')
+load('ext://my-extension', 'printFoo')
+printFoo()
+`, f.tmp.Path())
+
+	f.skf.File("Tiltfile.a", subfileContent)
+	f.skf.File("Tiltfile.b", subfileContent)
+	f.tiltfile(`
+include('Tiltfile.a')
+include('Tiltfile.b')
+`)
+	res := f.assertExecOutput("foo\nfoo")
+	f.assertLoadRecorded(res, "my-extension")
+}
+
 type extensionFixture struct {
 	t     *testing.T
 	skf   *starkit.Fixture
diff --git a/internal/tiltfile/v1alpha1/plugin.go b/internal/tiltfile/v1alpha1/plugin.go
index 94f97bc56b..c716ac4aca 100644
--- a/internal/tiltfile/v1alpha1/plugin.go
+++ b/internal/tiltfile/v1alpha1/plugin.go
@@ -10,6 +10,7 @@ import (
 	"github.com/tilt-dev/tilt/internal/controllers/apicmp"
 	"github.com/tilt-dev/tilt/internal/controllers/apiset"
 	"github.com/tilt-dev/tilt/internal/tiltfile/starkit"
+	"github.com/tilt-dev/tilt/pkg/apis/core/v1alpha1"
 )
 
 // Defines starlark functions that register API objects
@@ -47,8 +48,13 @@ func (p Plugin) register(t *starlark.Thread, obj apiset.Object) (starlark.Value,
 		typedSet := set.GetOrCreateTypedSet(obj)
 		name := obj.GetName()
 		existing, exists := typedSet[name]
-		if exists && !apicmp.DeepEqual(obj, existing) {
-			return set, fmt.Errorf("%s %q already registered", obj.GetGroupVersionResource().Resource, name)
+		if exists {
+			// tiltextension adds this for extensions, but new objects will not
+			// have this annotation yet, so delete for comparison
+			delete(existing.GetAnnotations(), v1alpha1.AnnotationManagedBy)
+			if !apicmp.DeepEqual(obj, existing) {
+				return set, fmt.Errorf("%s %q already registered", obj.GetGroupVersionResource().Resource, name)
+			}
 		}
 
 		typedSet[name] = obj