diff --git a/repo/fsrepo/datastores.go b/repo/fsrepo/datastores.go
index c5b81ce15..4d7306f56 100644
--- a/repo/fsrepo/datastores.go
+++ b/repo/fsrepo/datastores.go
@@ -31,14 +31,17 @@ type DatastoreConfig interface {
 	Create(path string) (repo.Datastore, error)
 }
 
-func (spec DiskSpec) String() string {
+func (spec DiskSpec) Bytes() []byte {
 	b, err := json.Marshal(spec)
 	if err != nil {
 		// should not happen
 		panic(err)
 	}
-	b = bytes.TrimSpace(b)
-	return string(b)
+	return bytes.TrimSpace(b)
+}
+
+func (spec DiskSpec) String() string {
+	return string(spec.Bytes())
 }
 
 var datastores map[string]ConfigFromMap
diff --git a/repo/fsrepo/fsrepo.go b/repo/fsrepo/fsrepo.go
index 44ef42382..b81052118 100644
--- a/repo/fsrepo/fsrepo.go
+++ b/repo/fsrepo/fsrepo.go
@@ -240,9 +240,29 @@ func initConfig(path string, conf *config.Config) error {
 	if err := serialize.WriteConfigFile(configFilename, conf); err != nil {
 		return err
 	}
+
 	return nil
 }
 
+func initSpec(path string, conf map[string]interface{}) error {
+	fn, err := config.Path(path, SpecFn)
+	if err != nil {
+		return err
+	}
+
+	if util.FileExists(fn) {
+		return nil
+	}
+
+	dsc, err := AnyDatastoreConfig(conf)
+	if err != nil {
+		return err
+	}
+	bytes := dsc.DiskSpec().Bytes()
+
+	return ioutil.WriteFile(fn, bytes, 0600)
+}
+
 // Init initializes a new FSRepo at the given path with the provided config.
 // TODO add support for custom datastores.
 func Init(repoPath string, conf *config.Config) error {
@@ -260,6 +280,10 @@ func Init(repoPath string, conf *config.Config) error {
 		return err
 	}
 
+	if err := initSpec(repoPath, conf.Datastore.Spec); err != nil {
+		return err
+	}
+
 	if err := mfsr.RepoPath(repoPath).WriteVersion(RepoVersion); err != nil {
 		return err
 	}
@@ -370,19 +394,13 @@ func (r *FSRepo) openDatastore() error {
 	spec := dsc.DiskSpec()
 
 	oldSpec, err := r.readSpec()
-	if err == nil {
-		if oldSpec != spec.String() {
-			return fmt.Errorf("Datastore configuration of '%s' does not match what is on disk '%s'",
-				oldSpec, spec.String())
-		}
-	} else if os.IsNotExist(err) {
-		err := r.writeSpec(spec.String())
-		if err != nil {
-			return err
-		}
-	} else {
+	if err != nil {
 		return err
 	}
+	if oldSpec != spec.String() {
+		return fmt.Errorf("Datastore configuration of '%s' does not match what is on disk '%s'",
+			oldSpec, spec.String())
+	}
 
 	d, err := dsc.Create(r.path)
 	if err != nil {
@@ -411,19 +429,6 @@ func (r *FSRepo) readSpec() (string, error) {
 	return strings.TrimSpace(string(b)), nil
 }
 
-func (r *FSRepo) writeSpec(spec string) error {
-	fn, err := config.Path(r.path, SpecFn)
-	if err != nil {
-		return err
-	}
-	b := []byte(spec)
-	err = ioutil.WriteFile(fn, b, 0600)
-	if err != nil {
-		return err
-	}
-	return nil
-}
-
 // Close closes the FSRepo, releasing held resources.
 func (r *FSRepo) Close() error {
 	packageLock.Lock()
diff --git a/repo/fsrepo/fsrepo_test.go b/repo/fsrepo/fsrepo_test.go
index c886db1d6..73ae54ab2 100644
--- a/repo/fsrepo/fsrepo_test.go
+++ b/repo/fsrepo/fsrepo_test.go
@@ -25,7 +25,7 @@ func TestInitIdempotence(t *testing.T) {
 	t.Parallel()
 	path := testRepoPath("", t)
 	for i := 0; i < 10; i++ {
-		assert.Nil(Init(path, &config.Config{}), t, "multiple calls to init should succeed")
+		assert.Nil(Init(path, &config.Config{Datastore: config.DefaultDatastoreConfig()}), t, "multiple calls to init should succeed")
 	}
 }