diff --git a/hugegraph-server/hugegraph-hbase/src/main/java/org/apache/hugegraph/backend/store/hbase/HbaseStore.java b/hugegraph-server/hugegraph-hbase/src/main/java/org/apache/hugegraph/backend/store/hbase/HbaseStore.java
index 1d75c00944..56f7210cc8 100644
--- a/hugegraph-server/hugegraph-hbase/src/main/java/org/apache/hugegraph/backend/store/hbase/HbaseStore.java
+++ b/hugegraph-server/hugegraph-hbase/src/main/java/org/apache/hugegraph/backend/store/hbase/HbaseStore.java
@@ -114,6 +114,15 @@ protected List<String> tableNames() {
                           .collect(Collectors.toList());
     }
 
+    /**
+     * The tables to truncate when the graph is cleared, all the tables of
+     * the store by default. A store that keeps backend metadata which must
+     * survive a clear excludes it here, see {@link HbaseSystemStore}.
+     */
+    protected List<String> tableNamesToTruncate() {
+        return this.tableNames();
+    }
+
     public String namespace() {
         return this.namespace;
     }
@@ -371,7 +380,7 @@ public void truncate() {
         };
 
         // Truncate tables
-        List<String> tables = this.tableNames();
+        List<String> tables = this.tableNamesToTruncate();
         Map<String, Future<Void>> futures = new HashMap<>(tables.size());
 
         try {
@@ -383,7 +392,7 @@ public void truncate() {
                 wait.apply(entry.getKey(), entry.getValue());
             }
         } catch (Exception e) {
-            this.enableTables();
+            this.enableTables(tables);
             throw new BackendException(
                     "Failed to disable table for '%s' store", e, this.store);
         }
@@ -397,7 +406,7 @@ public void truncate() {
                 wait.apply(entry.getKey(), entry.getValue());
             }
         } catch (Exception e) {
-            this.enableTables();
+            this.enableTables(tables);
             throw new BackendException(
                     "Failed to truncate table for '%s' store", e, this.store);
         }
@@ -405,8 +414,8 @@ public void truncate() {
         LOG.debug("Store truncated: {}", this.store);
     }
 
-    private void enableTables() {
-        for (String table : this.tableNames()) {
+    private void enableTables(List<String> tables) {
+        for (String table : tables) {
             try {
                 this.sessions.enableTable(table);
             } catch (Exception e) {
@@ -575,6 +584,18 @@ protected List<String> tableNames() {
             return tableNames;
         }
 
+        @Override
+        protected List<String> tableNamesToTruncate() {
+            /*
+             * Keep the meta table: it holds the backend version written by
+             * init(), truncating it makes the version check fail at the next
+             * startup (see #2209)
+             */
+            List<String> tableNames = this.tableNames();
+            tableNames.remove(this.meta.table());
+            return tableNames;
+        }
+
         @Override
         public void init() {
             super.init();
diff --git a/hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/core/MultiGraphsTest.java b/hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/core/MultiGraphsTest.java
index 70aa5df7d0..7ed172acd9 100644
--- a/hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/core/MultiGraphsTest.java
+++ b/hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/core/MultiGraphsTest.java
@@ -71,6 +71,56 @@ public void testWriteAndReadVersion() {
         destroyGraphs(graphs);
     }
 
+    @Test
+    public void testTruncateBackendKeepsVersionAndResetsSchemaIds() {
+        // hstore keeps the schema in PD meta after truncate and caches id ranges
+        Assume.assumeFalse("skip this test for hstore",
+                           "hstore".equals(graph().backend()));
+
+        HugeGraph graph = openGraphs("truncate_g").get(0);
+        try {
+            // Start from a clean backend in case a previous run failed midway
+            graph.clearBackend();
+            graph.initBackend();
+            graph.serverStarted(GlobalMasterInfo.master("server-truncate"));
+
+            BackendStoreInfo backendStoreInfo = graph.backendStoreInfo();
+            Assert.assertTrue(backendStoreInfo.checkVersion());
+
+            SchemaManager schema = graph.schema();
+            schema.propertyKey("name").asText().create();
+            VertexLabel person = schema.vertexLabel("person")
+                                       .properties("name")
+                                       .useAutomaticId().create();
+            graph.addVertex(T.label, "person", "name", "marko");
+            graph.tx().commit();
+            Assert.assertEquals(1L, graph.traversal().V().count().next());
+
+            graph.truncateBackend();
+
+            // The backend version written by init() survives the truncate
+            Assert.assertTrue(backendStoreInfo.exists());
+            Assert.assertTrue(backendStoreInfo.checkVersion());
+            // The schema and the data are gone
+            Assert.assertEquals(0L, graph.traversal().V().count().next());
+            Assert.assertTrue(schema.getVertexLabels().isEmpty());
+            Assert.assertTrue(schema.getPropertyKeys().isEmpty());
+            // The schema id counters are reset: the same ids are handed out
+            schema.propertyKey("name").asText().create();
+            VertexLabel person2 = schema.vertexLabel("person")
+                                        .properties("name")
+                                        .useAutomaticId().create();
+            Assert.assertEquals(person.id(), person2.id());
+            graph.addVertex(T.label, "person", "name", "marko");
+            graph.tx().commit();
+            Assert.assertEquals(1L, graph.traversal().V().count().next());
+
+            graph.clearBackend();
+        } finally {
+            destroyGraphs(ImmutableList.of(graph));
+        }
+    }
+
     @Test
     public void testCreateMultiGraphs() {
         List<HugeGraph> graphs = openGraphs("g_1", NAME48);