diff --git a/flake.lock b/flake.lock
index fa5649c03..70a433b26 100644
--- a/flake.lock
+++ b/flake.lock
@@ -2,9 +2,10 @@
     "inputs": {
         "nixpkgs": {
             "inputs": {},
-            "narHash": "sha256-TrLhI3xPkTTznE9gcMHhkHirGNN7N02zM4DxJ/U3WRs=",
-            "uri": "github:edolstra/nixpkgs/24bf27fc215e8300877dfa1c426b9966bbfbd150"
+            "narHash": "sha256-HGlE2VNbdEjCP76hWAS72kHBlMWhpvqWo58Obg1Vy6s=",
+            "originalUri": "nixpkgs",
+            "uri": "github:edolstra/nixpkgs/13e1bce51f4aebdf3db58ce8c4a93e904a272bff"
         }
     },
-    "version": 2
+    "version": 3
 }
diff --git a/src/libexpr/flake/flake.cc b/src/libexpr/flake/flake.cc
index 050e65259..accdb4194 100644
--- a/src/libexpr/flake/flake.cc
+++ b/src/libexpr/flake/flake.cc
@@ -205,8 +205,10 @@ static void expectType(EvalState & state, ValueType type,
             showType(type), showType(value.type), pos);
 }
 
-Flake getFlake(EvalState & state, const FlakeRef & flakeRef)
+Flake getFlake(EvalState & state, const FlakeRef & originalRef, bool allowLookup)
 {
+    auto flakeRef = maybeLookupFlake(state, originalRef, allowLookup);
+
     SourceInfo sourceInfo = fetchFlake(state, flakeRef);
     debug("got flake source '%s' with flakeref %s", sourceInfo.storePath, sourceInfo.resolvedRef.to_string());
 
@@ -223,7 +225,7 @@ Flake getFlake(EvalState & state, const FlakeRef & flakeRef)
     if (!isInDir(realFlakeFile, state.store->toRealPath(sourceInfo.storePath)))
         throw Error("'flake.nix' file of flake '%s' escapes from '%s'", resolvedRef, sourceInfo.storePath);
 
-    Flake flake(flakeRef, sourceInfo);
+    Flake flake(originalRef, sourceInfo);
 
     if (!pathExists(realFlakeFile))
         throw Error("source tree referenced by '%s' does not contain a '%s/flake.nix' file", resolvedRef, resolvedRef.subdir);
@@ -358,6 +360,7 @@ bool allowedToUseRegistries(HandleLockFile handle, bool isTopRef)
    Note that this is lazy: we only recursively fetch inputs that are
    not in the lockfile yet. */
 static std::pair<Flake, LockedInput> updateLocks(
+    const std::string & inputPath,
     EvalState & state,
     const Flake & flake,
     HandleLockFile handleLockFile,
@@ -366,23 +369,36 @@ static std::pair<Flake, LockedInput> updateLocks(
 {
     LockedInput newEntry(
         flake.sourceInfo.resolvedRef,
+        flake.originalRef,
         flake.sourceInfo.narHash);
 
     for (auto & [id, input] : flake.inputs) {
+        auto inputPath2 = (inputPath.empty() ? "" : inputPath + "/") + id;
         auto i = oldEntry.inputs.find(id);
-        if (i != oldEntry.inputs.end()) {
+        if (i != oldEntry.inputs.end() && i->second.originalRef == input.ref) {
             newEntry.inputs.insert_or_assign(id, i->second);
         } else {
             if (handleLockFile == AllPure || handleLockFile == TopRefUsesRegistries)
                 throw Error("cannot update flake input '%s' in pure mode", id);
-            if (input.isFlake)
+            if (input.isFlake) {
+                auto actualInput = getFlake(state, input.ref,
+                        allowedToUseRegistries(handleLockFile, false));
+                if (i == oldEntry.inputs.end())
+                    printMsg(lvlWarn, "mapped flake input '%s' to '%s'",
+                        inputPath2, actualInput.sourceInfo.resolvedRef);
+                else
+                    printMsg(lvlWarn, "updated flake input '%s' from '%s' to '%s'",
+                        inputPath2, i->second.originalRef, actualInput.sourceInfo.resolvedRef);
                 newEntry.inputs.insert_or_assign(id,
-                    updateLocks(state,
-                        getFlake(state, maybeLookupFlake(state, input.ref, allowedToUseRegistries(handleLockFile, false))),
-                        handleLockFile, {}, false).second);
-            else {
-                auto sourceInfo = getNonFlake(state, maybeLookupFlake(state, input.ref, allowedToUseRegistries(handleLockFile, false)));
-                newEntry.inputs.insert_or_assign(id, LockedInput(sourceInfo.resolvedRef, sourceInfo.narHash));
+                    updateLocks(inputPath2, state, actualInput, handleLockFile, {}, false).second);
+            } else {
+                auto sourceInfo = getNonFlake(state,
+                    maybeLookupFlake(state, input.ref,
+                        allowedToUseRegistries(handleLockFile, false)));
+                printMsg(lvlWarn, "mapped flake input '%s' to '%s'",
+                    inputPath2, sourceInfo.resolvedRef);
+                newEntry.inputs.insert_or_assign(id,
+                    LockedInput(sourceInfo.resolvedRef, input.ref, sourceInfo.narHash));
             }
         }
     }
@@ -394,7 +410,8 @@ static std::pair<Flake, LockedInput> updateLocks(
    and optionally write it to file, it the flake is writable. */
 ResolvedFlake resolveFlake(EvalState & state, const FlakeRef & topRef, HandleLockFile handleLockFile)
 {
-    auto flake = getFlake(state, maybeLookupFlake(state, topRef, allowedToUseRegistries(handleLockFile, true)));
+    auto flake = getFlake(state, topRef,
+        allowedToUseRegistries(handleLockFile, true));
 
     LockFile oldLockFile;
 
@@ -407,7 +424,7 @@ ResolvedFlake resolveFlake(EvalState & state, const FlakeRef & topRef, HandleLoc
     }
 
     LockFile lockFile(updateLocks(
-            state, flake, handleLockFile, oldLockFile, true).second);
+            "", state, flake, handleLockFile, oldLockFile, true).second);
 
     if (!(lockFile == oldLockFile)) {
         if (allowedToWrite(handleLockFile)) {
@@ -476,7 +493,7 @@ static void prim_callFlake(EvalState & state, const Pos & pos, Value * * args, V
     assert(lazyInput->lockedInput.ref.isImmutable());
 
     if (lazyInput->isFlake) {
-        auto flake = getFlake(state, lazyInput->lockedInput.ref);
+        auto flake = getFlake(state, lazyInput->lockedInput.ref, false);
 
         if (flake.sourceInfo.narHash != lazyInput->lockedInput.narHash)
             throw Error("the content hash of flake '%s' doesn't match the hash recorded in the referring lockfile", flake.sourceInfo.resolvedRef);
diff --git a/src/libexpr/flake/flake.hh b/src/libexpr/flake/flake.hh
index 8f05e9799..b366e650b 100644
--- a/src/libexpr/flake/flake.hh
+++ b/src/libexpr/flake/flake.hh
@@ -78,7 +78,7 @@ struct Flake
         : originalRef(origRef), sourceInfo(sourceInfo) {};
 };
 
-Flake getFlake(EvalState &, const FlakeRef &);
+Flake getFlake(EvalState & state, const FlakeRef & flakeRef, bool allowLookup);
 
 /* If 'allowLookup' is true, then resolve 'flakeRef' using the
    registries. */
diff --git a/src/libexpr/flake/lockfile.cc b/src/libexpr/flake/lockfile.cc
index f32d752f9..039b7a7c1 100644
--- a/src/libexpr/flake/lockfile.cc
+++ b/src/libexpr/flake/lockfile.cc
@@ -6,6 +6,7 @@ namespace nix::flake {
 LockedInput::LockedInput(const nlohmann::json & json)
     : LockedInputs(json)
     , ref(json["uri"])
+    , originalRef(json["originalUri"])
     , narHash(Hash((std::string) json["narHash"]))
 {
     if (!ref.isImmutable())
@@ -16,6 +17,7 @@ nlohmann::json LockedInput::toJson() const
 {
     auto json = LockedInputs::toJson();
     json["uri"] = ref.to_string();
+    json["originalUri"] = originalRef.to_string();
     json["narHash"] = narHash.to_string(SRI);
     return json;
 }
@@ -54,7 +56,7 @@ bool LockedInputs::isDirty() const
 nlohmann::json LockFile::toJson() const
 {
     auto json = LockedInputs::toJson();
-    json["version"] = 2;
+    json["version"] = 3;
     return json;
 }
 
@@ -64,7 +66,7 @@ LockFile LockFile::read(const Path & path)
         auto json = nlohmann::json::parse(readFile(path));
 
         auto version = json.value("version", 0);
-        if (version != 2)
+        if (version != 3)
             throw Error("lock file '%s' has unsupported version %d", path, version);
 
         return LockFile(json);
diff --git a/src/libexpr/flake/lockfile.hh b/src/libexpr/flake/lockfile.hh
index 084eabc1a..ab81eac8b 100644
--- a/src/libexpr/flake/lockfile.hh
+++ b/src/libexpr/flake/lockfile.hh
@@ -30,11 +30,11 @@ struct LockedInputs
 /* Lock file information about a flake input. */
 struct LockedInput : LockedInputs
 {
-    FlakeRef ref;
+    FlakeRef ref, originalRef;
     Hash narHash;
 
-    LockedInput(const FlakeRef & ref, const Hash & narHash)
-        : ref(ref), narHash(narHash)
+    LockedInput(const FlakeRef & ref, const FlakeRef & originalRef, const Hash & narHash)
+        : ref(ref), originalRef(originalRef), narHash(narHash)
     {
         assert(ref.isImmutable());
     };
diff --git a/src/nix/flake.cc b/src/nix/flake.cc
index 5fd3f5508..599bf12eb 100644
--- a/src/nix/flake.cc
+++ b/src/nix/flake.cc
@@ -38,8 +38,7 @@ public:
     Flake getFlake()
     {
         auto evalState = getEvalState();
-        return flake::getFlake(*evalState,
-            maybeLookupFlake(*evalState, getFlakeRef(), useRegistries));
+        return flake::getFlake(*evalState, getFlakeRef(), useRegistries);
     }
 
     ResolvedFlake resolveFlake()
@@ -500,13 +499,13 @@ struct CmdFlakePin : virtual Args, EvalCommand
         FlakeRegistry userRegistry = *readRegistry(userRegistryPath);
         auto it = userRegistry.entries.find(FlakeRef(alias));
         if (it != userRegistry.entries.end()) {
-            it->second = getFlake(*evalState, maybeLookupFlake(*evalState, it->second, true)).sourceInfo.resolvedRef;
+            it->second = getFlake(*evalState, it->second, true).sourceInfo.resolvedRef;
             writeRegistry(userRegistry, userRegistryPath);
         } else {
             std::shared_ptr<FlakeRegistry> globalReg = evalState->getGlobalFlakeRegistry();
             it = globalReg->entries.find(FlakeRef(alias));
             if (it != globalReg->entries.end()) {
-                auto newRef = getFlake(*evalState, maybeLookupFlake(*evalState, it->second, true)).sourceInfo.resolvedRef;
+                auto newRef = getFlake(*evalState, it->second, true).sourceInfo.resolvedRef;
                 userRegistry.entries.insert_or_assign(alias, newRef);
                 writeRegistry(userRegistry, userRegistryPath);
             } else