diff --git a/src/OT/Color/COLR/COLR.hh b/src/OT/Color/COLR/COLR.hh
index 53c4ce0d4..6b5b104f3 100644
--- a/src/OT/Color/COLR/COLR.hh
+++ b/src/OT/Color/COLR/COLR.hh
@@ -2339,7 +2339,11 @@ struct COLR
                                   c->plan->colrv1_varstore_inner_maps.as_array ()))
         return_trace (false);
 
-      if (!out->varStore.serialize_serialize (c->serializer,
+      /* do not serialize varStore if there's no variation data after
+       * instancing: region_list or var_data is empty */
+      if (item_vars.get_region_list () &&
+          item_vars.get_vardata_encodings () &&
+          !out->varStore.serialize_serialize (c->serializer,
                                               item_vars.has_long_word (),
                                               c->plan->axis_tags,
                                               item_vars.get_region_list (),
@@ -2347,7 +2351,9 @@ struct COLR
         return_trace (false);
 
       /* if varstore is optimized, update colrv1_new_deltaset_idx_varidx_map in
-       * subset plan */
+       * subset plan.
+       * If varstore is empty after instancing, varidx_map would be empty and
+       * all var_idxes will be updated to VarIdx::NO_VARIATION */
       if (optimize)
       {
         const hb_map_t &varidx_map = item_vars.get_varidx_map ();
diff --git a/src/hb-ot-var-common.hh b/src/hb-ot-var-common.hh
index 7fc9b7c74..92b1caa17 100644
--- a/src/hb-ot-var-common.hh
+++ b/src/hb-ot-var-common.hh
@@ -1663,7 +1663,9 @@ struct item_variations_t
       }
     }
 
-    if (!all_regions || !all_unique_regions) return false;
+    /* regions are empty means no variation data, return true */
+    if (!all_regions || !all_unique_regions) return true;
+
     if (!region_list.alloc (all_regions.get_population ()))
       return false;
 
@@ -1728,7 +1730,8 @@ struct item_variations_t
 
   bool as_item_varstore (bool optimize=true, bool use_no_variation_idx=true)
   {
-    if (!region_list) return false;
+    /* return true if no variation data */
+    if (!region_list) return true;
     unsigned num_cols = region_list.length;
     /* pre-alloc a 2D vector for all sub_table's VarData rows */
     unsigned total_rows = 0;
diff --git a/test/subset/data/expected/colrv1_partial_instance/sixtyfour_subset.default.all.SCAN=0,XELA=0,YELA=0.ttf b/test/subset/data/expected/colrv1_partial_instance/sixtyfour_subset.default.all.SCAN=0,XELA=0,YELA=0.ttf
new file mode 100644
index 000000000..235d83d9f
Binary files /dev/null and b/test/subset/data/expected/colrv1_partial_instance/sixtyfour_subset.default.all.SCAN=0,XELA=0,YELA=0.ttf differ
diff --git a/test/subset/data/fonts/sixtyfour_subset.ttf b/test/subset/data/fonts/sixtyfour_subset.ttf
new file mode 100644
index 000000000..031810695
Binary files /dev/null and b/test/subset/data/fonts/sixtyfour_subset.ttf differ
diff --git a/test/subset/data/tests/colrv1_partial_instance.tests b/test/subset/data/tests/colrv1_partial_instance.tests
new file mode 100644
index 000000000..e7034af4f
--- /dev/null
+++ b/test/subset/data/tests/colrv1_partial_instance.tests
@@ -0,0 +1,14 @@
+FONTS:
+sixtyfour_subset.ttf
+
+PROFILES:
+default.txt
+
+SUBSETS:
+*
+
+INSTANCES:
+SCAN=0,XELA=0,YELA=0
+
+OPTIONS:
+no_fonttools
diff --git a/test/subset/meson.build b/test/subset/meson.build
index b94464ed7..b35489329 100644
--- a/test/subset/meson.build
+++ b/test/subset/meson.build
@@ -78,6 +78,7 @@ tests = [
   'feature_variation_instance_collect_lookups',
   'sync_vmetrics',
   'empty_region_vardata',
+  'colrv1_partial_instance',
 ]
 
 if get_option('experimental_api')