diff --git a/ChangeLog.md b/ChangeLog.md
index e99c828fa5..be571e045a 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -31,6 +31,7 @@ Behavior changes:
 
 * We now recommend checking in generated cabal files for repos. When generating lock files for
   extra-deps that only include `package.yaml` files, a deprecation warning will be generated.
+  Also, those packages will no longer be included in the generated lock files.
   See [#5210](https://github.com/commercialhaskell/stack/issues/5210).
 
 Other enhancements:
diff --git a/package.yaml b/package.yaml
index 668457b831..4c29f9d331 100644
--- a/package.yaml
+++ b/package.yaml
@@ -92,7 +92,7 @@ dependencies:
 - network-uri
 - open-browser
 - optparse-applicative
-- pantry >= 0.3.1.0
+- pantry >= 0.4.0.0
 - casa-client
 - casa-types
 - path
diff --git a/src/Stack/Config.hs b/src/Stack/Config.hs
index 51f23f377e..85758abbfc 100644
--- a/src/Stack/Config.hs
+++ b/src/Stack/Config.hs
@@ -592,8 +592,17 @@ fillProjectWanted stackYamlFP config project locCache snapCompiler snapPackages
     (deps0, mcompleted) <- fmap unzip . forM (projectDependencies project) $ \rpl -> do
       (pl, mCompleted) <- case rpl of
          RPLImmutable rpli -> do
-           compl <- maybe (completePackageLocation rpli) pure (Map.lookup rpli locCache)
-           pure (PLImmutable compl, Just (CompletedPLI rpli compl))
+           (compl, mcompl) <-
+             case Map.lookup rpli locCache of
+               Just compl -> pure (compl, Just compl)
+               Nothing -> do
+                 cpl <- completePackageLocation rpli
+                 if cplHasCabalFile cpl
+                   then pure (cplComplete cpl, Just $ cplComplete cpl)
+                   else do
+                     warnMissingCabalFile rpli
+                     pure (cplComplete cpl, Nothing)
+           pure $ (PLImmutable compl, CompletedPLI rpli <$> mcompl)
          RPLMutable p ->
            pure (PLMutable p, Nothing)
       dp <- additionalDepPackage (shouldHaddockDeps bopts) pl
diff --git a/src/Stack/Init.hs b/src/Stack/Init.hs
index a145d3e07c..f920f75414 100644
--- a/src/Stack/Init.hs
+++ b/src/Stack/Init.hs
@@ -116,7 +116,8 @@ initProject currDir initOpts mresolver = do
           Map.mapMaybe (flip Map.lookup gpdByDir . resolvedAbsolute) rbundle
 
     deps <- for (Map.toList extraDeps) $ \(n, v) ->
-      PLImmutable <$> completePackageLocation (RPLIHackage (PackageIdentifierRevision n v CFILatest) Nothing)
+      (PLImmutable . cplComplete) <$>
+      completePackageLocation (RPLIHackage (PackageIdentifierRevision n v CFILatest) Nothing)
 
     let p = Project
             { projectUserMsg = if userMsg == "" then Nothing else Just userMsg
diff --git a/src/Stack/Unpack.hs b/src/Stack/Unpack.hs
index 5c5b5f9ad6..16309ae0a4 100644
--- a/src/Stack/Unpack.hs
+++ b/src/Stack/Unpack.hs
@@ -38,7 +38,7 @@ unpackPackages mSnapshot dest input = do
     let (errs1, (names, pirs1)) =
           fmap partitionEithers $ partitionEithers $ map parse input
     locs1 <- forM pirs1 $ \pir -> do
-      loc <- completePackageLocation $ RPLIHackage pir Nothing
+      loc <- fmap cplComplete $ completePackageLocation $ RPLIHackage pir Nothing
       pure (loc, packageLocationIdent loc)
     (errs2, locs2) <- partitionEithers <$> traverse toLoc names
     case errs1 ++ errs2 of
@@ -97,7 +97,7 @@ unpackPackages mSnapshot dest input = do
           Nothing ->
             pure $ Left $ "Package does not appear in snapshot: " ++ packageNameString name
           Just sp -> do
-            loc <- completePackageLocation (rspLocation sp)
+            loc <- cplComplete <$> completePackageLocation (rspLocation sp)
             pure $ Right (loc, packageLocationIdent loc)
 
     -- Possible future enhancement: parse names as name + version range
diff --git a/stack-ghc-84.yaml b/stack-ghc-84.yaml
index a24a9cdb2d..a0dd51d29c 100644
--- a/stack-ghc-84.yaml
+++ b/stack-ghc-84.yaml
@@ -40,7 +40,8 @@ extra-deps:
 - rio-prettyprint-0.1.0.0@rev:0
 - hi-file-parser-0.1.0.0@rev:0
 - http-download-0.2.0.0@rev:0
-- pantry-0.3.1.0@rev:0
+- github: commercialhaskell/pantry
+  commit: 400ae05722f1c3f5b8d9de46008a1fe6db325179
 - casa-client-0.0.1@rev:0
 - casa-types-0.0.1@rev:0
 - github: snoyberg/filelock
diff --git a/stack.cabal b/stack.cabal
index 97e231a6b8..766672b350 100644
--- a/stack.cabal
+++ b/stack.cabal
@@ -266,7 +266,7 @@ library
     , network-uri
     , open-browser
     , optparse-applicative
-    , pantry >=0.3.1.0
+    , pantry >=0.4.0.0
     , path
     , path-io
     , persistent
@@ -386,7 +386,7 @@ executable stack
     , network-uri
     , open-browser
     , optparse-applicative
-    , pantry >=0.3.1.0
+    , pantry >=0.4.0.0
     , path
     , path-io
     , persistent
@@ -505,7 +505,7 @@ executable stack-integration-test
     , open-browser
     , optparse-applicative
     , optparse-generic
-    , pantry >=0.3.1.0
+    , pantry >=0.4.0.0
     , path
     , path-io
     , persistent
@@ -627,7 +627,7 @@ test-suite stack-test
     , network-uri
     , open-browser
     , optparse-applicative
-    , pantry >=0.3.1.0
+    , pantry >=0.4.0.0
     , path
     , path-io
     , persistent
diff --git a/stack.yaml b/stack.yaml
index 1aeb444d05..bbb9ebd0db 100644
--- a/stack.yaml
+++ b/stack.yaml
@@ -26,7 +26,8 @@ extra-deps:
 - http-download-0.2.0.0@rev:0
 - github: snoyberg/filelock
   commit: 97e83ecc133cd60a99df8e1fa5a3c2739ad007dc
-- pantry-0.3.1.0@rev:0
+- github: commercialhaskell/pantry
+  commit: 400ae05722f1c3f5b8d9de46008a1fe6db325179
 - casa-client-0.0.1@rev:0
 - casa-types-0.0.1@rev:0