diff --git a/Lib/fontTools/subset/__init__.py b/Lib/fontTools/subset/__init__.py
index 14af6797b..e5857dd79 100644
--- a/Lib/fontTools/subset/__init__.py
+++ b/Lib/fontTools/subset/__init__.py
@@ -2407,12 +2407,27 @@ def prune_post_subset(self, options):
             for subr in subrs.items:
                 subr.subset_subroutines (local_subrs, font.GlobalSubrs)
 
+        # Delete local SubrsIndex if empty
+        if hasattr(font, 'FDSelect'):
+            for fd in font.FDArray:
+                _delete_empty_subrs(fd.Private)
+        else:
+            _delete_empty_subrs(font.Private)
+
         # Cleanup
         for subrs in all_subrs:
             del subrs._used, subrs._old_bias, subrs._new_bias
 
     return True
 
+
+def _delete_empty_subrs(private_dict):
+    if hasattr(private_dict, 'Subrs') and not private_dict.Subrs:
+        if 'Subrs' in private_dict.rawDict:
+            del private_dict.rawDict['Subrs']
+        del private_dict.Subrs
+
+
 @_add_method(ttLib.getTableClass('cmap'))
 def closure_glyphs(self, s):
     tables = [t for t in self.tables if t.isUnicode()]
diff --git a/Tests/subset/data/expect_desubroutinize_CFF.ttx b/Tests/subset/data/expect_desubroutinize_CFF.ttx
index ab08088b1..81b536904 100644
--- a/Tests/subset/data/expect_desubroutinize_CFF.ttx
+++ b/Tests/subset/data/expect_desubroutinize_CFF.ttx
@@ -33,9 +33,6 @@
         <initialRandomSeed value="0"/>
         <defaultWidthX value="267"/>
         <nominalWidthX value="448"/>
-        <Subrs>
-          <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-        </Subrs>
       </Private>
       <CharStrings>
         <CharString name=".notdef">
diff --git a/Tests/subset/data/expect_no_hinting_desubroutinize_CFF.ttx b/Tests/subset/data/expect_no_hinting_desubroutinize_CFF.ttx
index 149f09594..7f44c90fa 100644
--- a/Tests/subset/data/expect_no_hinting_desubroutinize_CFF.ttx
+++ b/Tests/subset/data/expect_no_hinting_desubroutinize_CFF.ttx
@@ -32,9 +32,6 @@
         <initialRandomSeed value="0"/>
         <defaultWidthX value="267"/>
         <nominalWidthX value="448"/>
-        <Subrs>
-          <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-        </Subrs>
       </Private>
       <CharStrings>
         <CharString name=".notdef">
diff --git a/Tests/subset/data/expect_no_notdef_outline_cid.ttx b/Tests/subset/data/expect_no_notdef_outline_cid.ttx
index 4e87cc126..5167c2cf1 100644
--- a/Tests/subset/data/expect_no_notdef_outline_cid.ttx
+++ b/Tests/subset/data/expect_no_notdef_outline_cid.ttx
@@ -43,9 +43,6 @@
             <initialRandomSeed value="0"/>
             <defaultWidthX value="1000"/>
             <nominalWidthX value="107"/>
-            <Subrs>
-              <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-            </Subrs>
           </Private>
         </FontDict>
       </FDArray>
diff --git a/Tests/subset/data/expect_no_notdef_outline_otf.ttx b/Tests/subset/data/expect_no_notdef_outline_otf.ttx
index 498a44b4e..22273c7c4 100644
--- a/Tests/subset/data/expect_no_notdef_outline_otf.ttx
+++ b/Tests/subset/data/expect_no_notdef_outline_otf.ttx
@@ -33,9 +33,6 @@
         <initialRandomSeed value="0"/>
         <defaultWidthX value="500"/>
         <nominalWidthX value="300"/>
-        <Subrs>
-          <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-        </Subrs>
       </Private>
       <CharStrings>
         <CharString name=".notdef">
diff --git a/Tests/subset/data/expect_notdef_width_cid.ttx b/Tests/subset/data/expect_notdef_width_cid.ttx
index c0bab754f..ccd0f65fc 100644
--- a/Tests/subset/data/expect_notdef_width_cid.ttx
+++ b/Tests/subset/data/expect_notdef_width_cid.ttx
@@ -38,9 +38,6 @@
             <initialRandomSeed value="0"/>
             <defaultWidthX value="602"/>
             <nominalWidthX value="630"/>
-            <Subrs>
-              <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-            </Subrs>
           </Private>
         </FontDict>
         <FontDict index="1">
@@ -56,9 +53,6 @@
             <initialRandomSeed value="0"/>
             <defaultWidthX value="1000"/>
             <nominalWidthX value="107"/>
-            <Subrs>
-              <!-- The 'index' attribute is only for humans; it is ignored when parsed. -->
-            </Subrs>
           </Private>
         </FontDict>
       </FDArray>