diff --git a/Lib/fontTools/feaLib/builder.py b/Lib/fontTools/feaLib/builder.py
index 63fd91182..7b6203684 100644
--- a/Lib/fontTools/feaLib/builder.py
+++ b/Lib/fontTools/feaLib/builder.py
@@ -555,10 +555,10 @@ class Builder(object):
                 alts.add(to_glyph)
             return
         if prefix or suffix:
+            chain = self.get_lookup_(location, ChainContextSubstBuilder)
             sub = self.get_chained_lookup_(location, SingleSubstBuilder)
             sub.mapping.update(mapping)
-            lookup = self.get_lookup_(location, ChainContextSubstBuilder)
-            lookup.substitutions.append(
+            chain.substitutions.append(
                 (prefix, [mapping.keys()], suffix, [sub]))
             return
         lookup = self.get_lookup_(location, SingleSubstBuilder)
diff --git a/Lib/fontTools/feaLib/testdata/GSUB_6.ttx b/Lib/fontTools/feaLib/testdata/GSUB_6.ttx
index 8e5173e2b..80f3bf03e 100644
--- a/Lib/fontTools/feaLib/testdata/GSUB_6.ttx
+++ b/Lib/fontTools/feaLib/testdata/GSUB_6.ttx
@@ -23,7 +23,7 @@
         <FeatureTag value="test"/>
         <Feature>
           <!-- LookupCount=5 -->
-          <LookupListIndex index="0" value="1"/>
+          <LookupListIndex index="0" value="0"/>
           <LookupListIndex index="1" value="3"/>
           <LookupListIndex index="2" value="5"/>
           <LookupListIndex index="3" value="7"/>
@@ -34,14 +34,6 @@
     <LookupList>
       <!-- LookupCount=10 -->
       <Lookup index="0">
-        <!-- LookupType=1 -->
-        <LookupFlag value="0"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="A" out="A.sc"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="1">
         <!-- LookupType=6 -->
         <LookupFlag value="0"/>
         <!-- SubTableCount=2 -->
@@ -62,7 +54,7 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="0"/>
+            <LookupListIndex value="1"/>
           </SubstLookupRecord>
         </ChainContextSubst>
         <ChainContextSubst index="1" Format="3">
@@ -88,6 +80,14 @@
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="1">
+        <!-- LookupType=1 -->
+        <LookupFlag value="0"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="A" out="A.sc"/>
+        </SingleSubst>
+      </Lookup>
       <Lookup index="2">
         <!-- LookupType=1 -->
         <LookupFlag value="0"/>
diff --git a/Lib/fontTools/feaLib/testdata/bug463.ttx b/Lib/fontTools/feaLib/testdata/bug463.ttx
index 7b025e7d4..0231fa670 100644
--- a/Lib/fontTools/feaLib/testdata/bug463.ttx
+++ b/Lib/fontTools/feaLib/testdata/bug463.ttx
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ttFont>
+<ttFont sfntVersion="true" ttLibVersion="3.0">
 
   <GSUB>
     <Version value="1.0"/>
@@ -23,22 +23,13 @@
         <FeatureTag value="ordn"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="1"/>
+          <LookupListIndex index="0" value="0"/>
         </Feature>
       </FeatureRecord>
     </FeatureList>
     <LookupList>
       <!-- LookupCount=3 -->
       <Lookup index="0">
-        <!-- LookupType=1 -->
-        <LookupFlag value="0"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="A" out="ordfeminine"/>
-          <Substitution in="a" out="ordfeminine"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="1">
         <!-- LookupType=6 -->
         <LookupFlag value="0"/>
         <!-- SubTableCount=2 -->
@@ -65,7 +56,7 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="0"/>
+            <LookupListIndex value="1"/>
           </SubstLookupRecord>
         </ChainContextSubst>
         <ChainContextSubst index="1" Format="3">
@@ -95,6 +86,15 @@
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="1">
+        <!-- LookupType=1 -->
+        <LookupFlag value="0"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="A" out="ordfeminine"/>
+          <Substitution in="a" out="ordfeminine"/>
+        </SingleSubst>
+      </Lookup>
       <Lookup index="2">
         <!-- LookupType=1 -->
         <LookupFlag value="0"/>
diff --git a/Lib/fontTools/feaLib/testdata/feature_aalt.ttx b/Lib/fontTools/feaLib/testdata/feature_aalt.ttx
index 01709fe52..f1db11f65 100644
--- a/Lib/fontTools/feaLib/testdata/feature_aalt.ttx
+++ b/Lib/fontTools/feaLib/testdata/feature_aalt.ttx
@@ -48,7 +48,7 @@
         <FeatureTag value="ordn"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="4"/>
+          <LookupListIndex index="0" value="3"/>
         </Feature>
       </FeatureRecord>
       <FeatureRecord index="4">
@@ -100,15 +100,6 @@
         </LigatureSubst>
       </Lookup>
       <Lookup index="3">
-        <!-- LookupType=1 -->
-        <LookupFlag value="0"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="A" out="ordfeminine"/>
-          <Substitution in="a" out="ordfeminine"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="4">
         <!-- LookupType=6 -->
         <LookupFlag value="0"/>
         <!-- SubTableCount=2 -->
@@ -135,7 +126,7 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="3"/>
+            <LookupListIndex value="4"/>
           </SubstLookupRecord>
         </ChainContextSubst>
         <ChainContextSubst index="1" Format="3">
@@ -165,6 +156,15 @@
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="4">
+        <!-- LookupType=1 -->
+        <LookupFlag value="0"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="A" out="ordfeminine"/>
+          <Substitution in="a" out="ordfeminine"/>
+        </SingleSubst>
+      </Lookup>
       <Lookup index="5">
         <!-- LookupType=1 -->
         <LookupFlag value="0"/>
diff --git a/Lib/fontTools/feaLib/testdata/spec5fi2.ttx b/Lib/fontTools/feaLib/testdata/spec5fi2.ttx
index 0bce0907a..45d70cd2d 100644
--- a/Lib/fontTools/feaLib/testdata/spec5fi2.ttx
+++ b/Lib/fontTools/feaLib/testdata/spec5fi2.ttx
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ttFont>
+<ttFont sfntVersion="true" ttLibVersion="3.0">
 
   <GSUB>
     <Version value="1.0"/>
@@ -23,21 +23,13 @@
         <FeatureTag value="test"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="1"/>
+          <LookupListIndex index="0" value="0"/>
         </Feature>
       </FeatureRecord>
     </FeatureList>
     <LookupList>
       <!-- LookupCount=2 -->
       <Lookup index="0">
-        <!-- LookupType=1 -->
-        <LookupFlag value="7"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="d" out="d.alt"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="1">
         <!-- LookupType=6 -->
         <LookupFlag value="7"/>
         <!-- SubTableCount=1 -->
@@ -56,10 +48,18 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="0"/>
+            <LookupListIndex value="1"/>
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="1">
+        <!-- LookupType=1 -->
+        <LookupFlag value="7"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="d" out="d.alt"/>
+        </SingleSubst>
+      </Lookup>
     </LookupList>
   </GSUB>
 
diff --git a/Lib/fontTools/feaLib/testdata/spec5fi3.ttx b/Lib/fontTools/feaLib/testdata/spec5fi3.ttx
index d4e33b78a..cba6725aa 100644
--- a/Lib/fontTools/feaLib/testdata/spec5fi3.ttx
+++ b/Lib/fontTools/feaLib/testdata/spec5fi3.ttx
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ttFont>
+<ttFont sfntVersion="true" ttLibVersion="3.0">
 
   <GSUB>
     <Version value="1.0"/>
@@ -23,46 +23,13 @@
         <FeatureTag value="test"/>
         <Feature>
           <!-- LookupCount=1 -->
-          <LookupListIndex index="0" value="1"/>
+          <LookupListIndex index="0" value="0"/>
         </Feature>
       </FeatureRecord>
     </FeatureList>
     <LookupList>
       <!-- LookupCount=2 -->
       <Lookup index="0">
-        <!-- LookupType=1 -->
-        <LookupFlag value="0"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="A.sc" out="a"/>
-          <Substitution in="B.sc" out="b"/>
-          <Substitution in="C.sc" out="c"/>
-          <Substitution in="D.sc" out="d"/>
-          <Substitution in="E.sc" out="e"/>
-          <Substitution in="F.sc" out="f"/>
-          <Substitution in="G.sc" out="g"/>
-          <Substitution in="H.sc" out="h"/>
-          <Substitution in="I.sc" out="i"/>
-          <Substitution in="J.sc" out="j"/>
-          <Substitution in="K.sc" out="k"/>
-          <Substitution in="L.sc" out="l"/>
-          <Substitution in="M.sc" out="m"/>
-          <Substitution in="N.sc" out="n"/>
-          <Substitution in="O.sc" out="o"/>
-          <Substitution in="P.sc" out="p"/>
-          <Substitution in="Q.sc" out="q"/>
-          <Substitution in="R.sc" out="r"/>
-          <Substitution in="S.sc" out="s"/>
-          <Substitution in="T.sc" out="t"/>
-          <Substitution in="U.sc" out="u"/>
-          <Substitution in="V.sc" out="v"/>
-          <Substitution in="W.sc" out="w"/>
-          <Substitution in="X.sc" out="x"/>
-          <Substitution in="Y.sc" out="y"/>
-          <Substitution in="Z.sc" out="z"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="1">
         <!-- LookupType=6 -->
         <LookupFlag value="0"/>
         <!-- SubTableCount=1 -->
@@ -129,10 +96,43 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="0"/>
+            <LookupListIndex value="1"/>
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="1">
+        <!-- LookupType=1 -->
+        <LookupFlag value="0"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="A.sc" out="a"/>
+          <Substitution in="B.sc" out="b"/>
+          <Substitution in="C.sc" out="c"/>
+          <Substitution in="D.sc" out="d"/>
+          <Substitution in="E.sc" out="e"/>
+          <Substitution in="F.sc" out="f"/>
+          <Substitution in="G.sc" out="g"/>
+          <Substitution in="H.sc" out="h"/>
+          <Substitution in="I.sc" out="i"/>
+          <Substitution in="J.sc" out="j"/>
+          <Substitution in="K.sc" out="k"/>
+          <Substitution in="L.sc" out="l"/>
+          <Substitution in="M.sc" out="m"/>
+          <Substitution in="N.sc" out="n"/>
+          <Substitution in="O.sc" out="o"/>
+          <Substitution in="P.sc" out="p"/>
+          <Substitution in="Q.sc" out="q"/>
+          <Substitution in="R.sc" out="r"/>
+          <Substitution in="S.sc" out="s"/>
+          <Substitution in="T.sc" out="t"/>
+          <Substitution in="U.sc" out="u"/>
+          <Substitution in="V.sc" out="v"/>
+          <Substitution in="W.sc" out="w"/>
+          <Substitution in="X.sc" out="x"/>
+          <Substitution in="Y.sc" out="y"/>
+          <Substitution in="Z.sc" out="z"/>
+        </SingleSubst>
+      </Lookup>
     </LookupList>
   </GSUB>
 
diff --git a/Lib/fontTools/feaLib/testdata/spec8a.ttx b/Lib/fontTools/feaLib/testdata/spec8a.ttx
index 579ca1400..14d085d2e 100644
--- a/Lib/fontTools/feaLib/testdata/spec8a.ttx
+++ b/Lib/fontTools/feaLib/testdata/spec8a.ttx
@@ -70,7 +70,7 @@
         <Feature>
           <!-- LookupCount=3 -->
           <LookupListIndex index="0" value="4"/>
-          <LookupListIndex index="1" value="6"/>
+          <LookupListIndex index="1" value="5"/>
           <LookupListIndex index="2" value="7"/>
         </Feature>
       </FeatureRecord>
@@ -151,16 +151,6 @@
         </AlternateSubst>
       </Lookup>
       <Lookup index="5">
-        <!-- LookupType=1 -->
-        <LookupFlag value="0"/>
-        <!-- SubTableCount=1 -->
-        <SingleSubst index="0">
-          <Substitution in="c" out="c.mid"/>
-          <Substitution in="d" out="d.mid"/>
-          <Substitution in="e" out="e.mid"/>
-        </SingleSubst>
-      </Lookup>
-      <Lookup index="6">
         <!-- LookupType=6 -->
         <LookupFlag value="0"/>
         <!-- SubTableCount=1 -->
@@ -182,10 +172,20 @@
           <!-- SubstCount=1 -->
           <SubstLookupRecord index="0">
             <SequenceIndex value="0"/>
-            <LookupListIndex value="5"/>
+            <LookupListIndex value="6"/>
           </SubstLookupRecord>
         </ChainContextSubst>
       </Lookup>
+      <Lookup index="6">
+        <!-- LookupType=1 -->
+        <LookupFlag value="0"/>
+        <!-- SubTableCount=1 -->
+        <SingleSubst index="0">
+          <Substitution in="c" out="c.mid"/>
+          <Substitution in="d" out="d.mid"/>
+          <Substitution in="e" out="e.mid"/>
+        </SingleSubst>
+      </Lookup>
       <Lookup index="7">
         <!-- LookupType=1 -->
         <LookupFlag value="0"/>