diff --git a/common/flatpak-dir.c b/common/flatpak-dir.c
index 8542300e..8595dafd 100644
--- a/common/flatpak-dir.c
+++ b/common/flatpak-dir.c
@@ -280,6 +280,23 @@ parse_storage_type (const char *type_string)
   return FLATPAK_DIR_STORAGE_TYPE_DEFAULT;
 }
 
+static gboolean
+has_system_location (GPtrArray  *locations,
+                     const char *id)
+{
+  int i;
+
+  for (i = 0; i < locations->len; i++)
+    {
+      GFile *path = g_ptr_array_index (locations, i);
+      DirExtraData *extra_data = g_object_get_data (G_OBJECT (path), "extra-data");
+      if (extra_data != NULL && g_strcmp0 (extra_data->id, id) == 0)
+        return TRUE;
+    }
+
+  return FALSE;
+}
+
 static gboolean
 append_locations_from_config_file (GPtrArray    *locations,
                                    const char   *file_path,
@@ -322,6 +339,12 @@ append_locations_from_config_file (GPtrArray    *locations,
       if (len > 0)
         id[len - 1] = '\0';
 
+      if (has_system_location (locations, id))
+        {
+          g_warning ("Found duplicate flatpak installation (Id: %s). Ignoring", id);
+          continue;
+        }
+
       path = g_key_file_get_string (keyfile, groups[i], "Path", &my_error);
       if (path == NULL)
         {