diff --git a/Lib/fontTools/varLib/featureVars.py b/Lib/fontTools/varLib/featureVars.py
index d5735776e..58fb3b6e6 100644
--- a/Lib/fontTools/varLib/featureVars.py
+++ b/Lib/fontTools/varLib/featureVars.py
@@ -7,6 +7,7 @@ from fontTools.misc.dictTools import hashdict
 from fontTools.misc.intTools import popCount
 from fontTools.ttLib import newTable
 from fontTools.ttLib.tables import otTables as ot
+from fontTools.ttLib.ttVisitor import TTVisitor
 from fontTools.otlLib.builder import buildLookup, buildSingleSubstSubtable
 from collections import OrderedDict
 
@@ -356,7 +357,7 @@ def addFeatureVariationsRaw(font, table, conditionalSubstitutions, featureTag='r
         records = []
         for varFeatureIndex in varFeatureIndices:
             existingLookupIndices = table.FeatureList.FeatureRecord[varFeatureIndex].Feature.LookupListIndex
-            records.append(buildFeatureTableSubstitutionRecord(varFeatureIndex, existingLookupIndices + lookupIndices))
+            records.append(buildFeatureTableSubstitutionRecord(varFeatureIndex, lookupIndices + existingLookupIndices))
         featureVariationRecords.append(buildFeatureVariationRecord(conditionTable, records))
 
     table.FeatureVariations = buildFeatureVariations(featureVariationRecords)
@@ -414,19 +415,44 @@ def makeSubstitutionsHashable(conditionalSubstitutions):
         condSubst.append((conditionSet, substitutions))
     return condSubst, sorted(allSubstitutions)
 
+class ShifterVisitor(TTVisitor):
+    def __init__(self, shift):
+        self.shift = shift
+
+@ShifterVisitor.register_attr(ot.Feature, "LookupListIndex")  # GSUB/GPOS
+def visit(visitor, obj, attr, value):
+    shift = visitor.shift
+    value = [l + shift for l in value]
+    setattr(obj, attr, value)
+
+@ShifterVisitor.register_attr(
+    (ot.SubstLookupRecord, ot.PosLookupRecord),
+    "LookupListIndex"
+)
+def visit(visitor, obj, attr, value):
+    setattr(obj, attr, visitor.shift + value)
 
 def buildSubstitutionLookups(gsub, allSubstitutions):
     """Build the lookups for the glyph substitutions, return a dict mapping
     the substitution to lookup indices."""
-    firstIndex = len(gsub.LookupList.Lookup)
+
+    # Insert lookups at the beginning of the lookup vector
+    # https://github.com/googlefonts/fontmake/issues/950
+
     lookupMap = {}
     for i, substitutionMap in enumerate(allSubstitutions):
-        lookupMap[substitutionMap] = i + firstIndex
+        lookupMap[substitutionMap] = i
 
-    for subst in allSubstitutions:
+    # Shift all lookup indices in gsub by len(allSubstitutions)
+    shift = len(allSubstitutions)
+    visitor = ShifterVisitor(shift)
+    visitor.visit(gsub.FeatureList.FeatureRecord)
+    visitor.visit(gsub.LookupList.Lookup)
+
+    for i, subst in enumerate(allSubstitutions):
         substMap = dict(subst)
         lookup = buildLookup([buildSingleSubstSubtable(substMap)])
-        gsub.LookupList.Lookup.append(lookup)
+        gsub.LookupList.Lookup.insert(i, lookup)
         assert gsub.LookupList.Lookup[lookupMap[subst]] is lookup
     gsub.LookupList.LookupCount = len(gsub.LookupList.Lookup)
     return lookupMap
diff --git a/Tests/varLib/data/test_results/FeatureVars_rclt.ttx b/Tests/varLib/data/test_results/FeatureVars_rclt.ttx
index b889f3a5f..e930ce72f 100644
--- a/Tests/varLib/data/test_results/FeatureVars_rclt.ttx
+++ b/Tests/varLib/data/test_results/FeatureVars_rclt.ttx
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ttFont sfntVersion="\x00\x01\x00\x00" ttLibVersion="3.29">
+<ttFont sfntVersion="\x00\x01\x00\x00" ttLibVersion="4.38">
 
   <fvar>
 
@@ -54,14 +54,14 @@
         <FeatureTag value="rclt"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="0"/>
+          <LookupListIndex index="0" value="3"/>
         </Feature>
       </FeatureRecord>
       <FeatureRecord index="1">
         <FeatureTag value="rclt"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="1"/>
+          <LookupListIndex index="0" value="4"/>
         </Feature>
       </FeatureRecord>
     </FeatureList>
@@ -72,7 +72,7 @@
         <LookupFlag value="0"/>
         <!-- SubTableCount=1 -->
         <SingleSubst index="0">
-          <Substitution in="uni0041" out="uni0061"/>
+          <Substitution in="uni0024" out="uni0024.nostroke"/>
         </SingleSubst>
       </Lookup>
       <Lookup index="1">
@@ -88,7 +88,7 @@
         <LookupFlag value="0"/>
         <!-- SubTableCount=1 -->
         <SingleSubst index="0">
-          <Substitution in="uni0024" out="uni0024.nostroke"/>
+          <Substitution in="uni0061" out="uni0041"/>
         </SingleSubst>
       </Lookup>
       <Lookup index="3">
@@ -104,7 +104,7 @@
         <LookupFlag value="0"/>
         <!-- SubTableCount=1 -->
         <SingleSubst index="0">
-          <Substitution in="uni0061" out="uni0041"/>
+          <Substitution in="uni0041" out="uni0061"/>
         </SingleSubst>
       </Lookup>
     </LookupList>
@@ -133,7 +133,7 @@
             <Feature>
               <!-- LookupCount=3 -->
               <LookupListIndex index="0" value="0"/>
-              <LookupListIndex index="1" value="2"/>
+              <LookupListIndex index="1" value="1"/>
               <LookupListIndex index="2" value="3"/>
             </Feature>
           </SubstitutionRecord>
@@ -141,9 +141,9 @@
             <FeatureIndex value="1"/>
             <Feature>
               <!-- LookupCount=3 -->
-              <LookupListIndex index="0" value="1"/>
-              <LookupListIndex index="1" value="2"/>
-              <LookupListIndex index="2" value="3"/>
+              <LookupListIndex index="0" value="0"/>
+              <LookupListIndex index="1" value="1"/>
+              <LookupListIndex index="2" value="4"/>
             </Feature>
           </SubstitutionRecord>
         </FeatureTableSubstitution>
@@ -169,15 +169,15 @@
             <FeatureIndex value="0"/>
             <Feature>
               <!-- LookupCount=2 -->
-              <LookupListIndex index="0" value="0"/>
-              <LookupListIndex index="1" value="4"/>
+              <LookupListIndex index="0" value="2"/>
+              <LookupListIndex index="1" value="3"/>
             </Feature>
           </SubstitutionRecord>
           <SubstitutionRecord index="1">
             <FeatureIndex value="1"/>
             <Feature>
               <!-- LookupCount=2 -->
-              <LookupListIndex index="0" value="1"/>
+              <LookupListIndex index="0" value="2"/>
               <LookupListIndex index="1" value="4"/>
             </Feature>
           </SubstitutionRecord>
@@ -199,7 +199,7 @@
             <FeatureIndex value="0"/>
             <Feature>
               <!-- LookupCount=2 -->
-              <LookupListIndex index="0" value="0"/>
+              <LookupListIndex index="0" value="1"/>
               <LookupListIndex index="1" value="3"/>
             </Feature>
           </SubstitutionRecord>
@@ -208,7 +208,7 @@
             <Feature>
               <!-- LookupCount=2 -->
               <LookupListIndex index="0" value="1"/>
-              <LookupListIndex index="1" value="3"/>
+              <LookupListIndex index="1" value="4"/>
             </Feature>
           </SubstitutionRecord>
         </FeatureTableSubstitution>
@@ -230,15 +230,15 @@
             <Feature>
               <!-- LookupCount=2 -->
               <LookupListIndex index="0" value="0"/>
-              <LookupListIndex index="1" value="2"/>
+              <LookupListIndex index="1" value="3"/>
             </Feature>
           </SubstitutionRecord>
           <SubstitutionRecord index="1">
             <FeatureIndex value="1"/>
             <Feature>
               <!-- LookupCount=2 -->
-              <LookupListIndex index="0" value="1"/>
-              <LookupListIndex index="1" value="2"/>
+              <LookupListIndex index="0" value="0"/>
+              <LookupListIndex index="1" value="4"/>
             </Feature>
           </SubstitutionRecord>
         </FeatureTableSubstitution>