diff --git a/google/metadata.go b/google/metadata.go
index 230b7a16..0d7aa00d 100644
--- a/google/metadata.go
+++ b/google/metadata.go
@@ -76,19 +76,6 @@ func MetadataUpdate(oldMDMap map[string]interface{}, newMDMap map[string]interfa
 	}
 }
 
-// Format metadata from the server data format -> schema data format
-func MetadataFormatSchema(curMDMap map[string]interface{}, md *compute.Metadata) map[string]interface{} {
-	newMD := make(map[string]interface{})
-
-	for _, kv := range md.Items {
-		if _, ok := curMDMap[kv.Key]; ok {
-			newMD[kv.Key] = *kv.Value
-		}
-	}
-
-	return newMD
-}
-
 // flattenComputeMetadata transforms a list of MetadataItems (as returned via the GCP client) into a simple map from key
 // to value.
 func flattenComputeMetadata(metadata []*compute.MetadataItems) map[string]string {
diff --git a/google/resource_compute_instance.go b/google/resource_compute_instance.go
index b1454eac..7462a85d 100644
--- a/google/resource_compute_instance.go
+++ b/google/resource_compute_instance.go
@@ -843,17 +843,25 @@ func resourceComputeInstanceRead(d *schema.ResourceData, meta interface{}) error
 		return err
 	}
 
-	// Synch metadata
-	md := instance.Metadata
+	md := flattenMetadata(instance.Metadata)
 
-	_md := MetadataFormatSchema(d.Get("metadata").(map[string]interface{}), md)
-
-	if script, scriptExists := d.GetOk("metadata_startup_script"); scriptExists {
-		d.Set("metadata_startup_script", script)
-		delete(_md, "startup-script")
+	if _, scriptExists := d.GetOk("metadata_startup_script"); scriptExists {
+		d.Set("metadata_startup_script", md["startup-script"])
+		// Note that here we delete startup-script from our metadata list. This is to prevent storing the startup-script
+		// as a value in the metadata since the config specifically tracks it under 'metadata_startup_script'
+		delete(md, "startup-script")
 	}
 
-	if err = d.Set("metadata", _md); err != nil {
+	existingMetadata := d.Get("metadata").(map[string]interface{})
+
+	// Delete any keys not explicitly set in our config file
+	for k := range md {
+		if _, ok := existingMetadata[k]; !ok {
+			delete(md, k)
+		}
+	}
+
+	if err = d.Set("metadata", md); err != nil {
 		return fmt.Errorf("Error setting metadata: %s", err)
 	}
 
diff --git a/google/resource_compute_project_metadata.go b/google/resource_compute_project_metadata.go
index 05919eb3..1814a637 100644
--- a/google/resource_compute_project_metadata.go
+++ b/google/resource_compute_project_metadata.go
@@ -102,9 +102,16 @@ func resourceComputeProjectMetadataRead(d *schema.ResourceData, meta interface{}
 		return handleNotFoundError(err, d, fmt.Sprintf("Project metadata for project %q", projectID))
 	}
 
-	md := project.CommonInstanceMetadata
+	md := flattenMetadata(project.CommonInstanceMetadata)
+	existingMetadata := d.Get("metadata").(map[string]interface{})
+	// Remove all keys not explicitly mentioned in the terraform config
+	for k := range md {
+		if _, ok := existingMetadata[k]; !ok {
+			delete(md, k)
+		}
+	}
 
-	if err = d.Set("metadata", MetadataFormatSchema(d.Get("metadata").(map[string]interface{}), md)); err != nil {
+	if err = d.Set("metadata", md); err != nil {
 		return fmt.Errorf("Error setting metadata: %s", err)
 	}