diff --git a/src/libexpr/flake/flake.cc b/src/libexpr/flake/flake.cc
index 39fdc776c..5018b460b 100644
--- a/src/libexpr/flake/flake.cc
+++ b/src/libexpr/flake/flake.cc
@@ -579,22 +579,23 @@ LockedFlake lockFlake(
 
                     newLockFile.write(path);
 
-                    // Rewriting the lockfile changed the top-level
-                    // repo, so we should re-read it.
+                    topRef.input->markChangedFile(
+                        (topRef.subdir == "" ? "" : topRef.subdir + "/") + "flake.lock");
+
+                    /* Rewriting the lockfile changed the top-level
+                       repo, so we should re-read it. FIXME: we could
+                       also just clear the 'rev' field... */
+                    auto prevLockedRef = flake.lockedRef;
                     FlakeCache dummyCache;
                     flake = getFlake(state, topRef, {}, lockFlags.useRegistries, dummyCache);
 
-                    if (flake.lockedRef.input->isImmutable())
+                    /* Make sure that we picked up the change,
+                       i.e. the tree should usually be dirty
+                       now. Corner case: we could have reverted from a
+                       dirty to a clean tree! */
+                    if (flake.lockedRef.input == prevLockedRef.input
+                        && !flake.lockedRef.input->isImmutable())
                         throw Error("'%s' did not change after I updated its 'flake.lock' file; is 'flake.lock' under version control?", flake.originalRef);
-
-                    #if 0
-                    // Hack: Make sure that flake.lock is visible to Git, so it ends up in the Nix store.
-                    runProgram("git", true,
-                        { "-C", *sourcePath, "add",
-                          "--force",
-                          "--intent-to-add",
-                          (topRef.subdir == "" ? "" : topRef.subdir + "/") + "flake.lock" });
-                    #endif
                 }
             } else
                 throw Error("cannot write modified lock file of flake '%s' (use '--no-write-lock-file' to ignore)", topRef);
diff --git a/src/libstore/fetchers/fetchers.hh b/src/libstore/fetchers/fetchers.hh
index 0ef79bc45..64628d1bb 100644
--- a/src/libstore/fetchers/fetchers.hh
+++ b/src/libstore/fetchers/fetchers.hh
@@ -62,6 +62,9 @@ struct Input : std::enable_shared_from_this<Input>
 
     virtual std::optional<Path> getSourcePath() const { return {}; }
 
+    // FIXME: should merge with getSourcePath().
+    virtual void markChangedFile(std::string_view file) const { assert(false); }
+
     virtual void clone(const Path & destDir) const
     {
         throw Error("do not know how to clone input '%s'", to_string());
diff --git a/src/libstore/fetchers/git.cc b/src/libstore/fetchers/git.cc
index 0101744bd..1c74d92a4 100644
--- a/src/libstore/fetchers/git.cc
+++ b/src/libstore/fetchers/git.cc
@@ -165,6 +165,18 @@ struct GitInput : Input
         return {};
     }
 
+    void markChangedFile(std::string_view file) const override
+    {
+        auto sourcePath = getSourcePath();
+        assert(sourcePath);
+        runProgram("git", true,
+            { "-C", *sourcePath, "add",
+              "--force",
+              "--intent-to-add",
+              std::string(file)
+            });
+    }
+
     std::pair<bool, std::string> getActualUrl() const
     {
         // Don't clone file:// URIs (but otherwise treat them the
diff --git a/src/libstore/fetchers/mercurial.cc b/src/libstore/fetchers/mercurial.cc
index 9b8c2132c..0825f6b23 100644
--- a/src/libstore/fetchers/mercurial.cc
+++ b/src/libstore/fetchers/mercurial.cc
@@ -84,6 +84,17 @@ struct MercurialInput : Input
         return {};
     }
 
+    void markChangedFile(std::string_view file) const override
+    {
+        auto sourcePath = getSourcePath();
+        assert(sourcePath);
+        // FIXME: shut up if file is already tracked.
+        runProgram("hg", true,
+            { "add",
+              *sourcePath + "/" + std::string(file)
+            });
+    }
+
     std::pair<bool, std::string> getActualUrl() const
     {
         bool isLocal = url.scheme == "file";
diff --git a/tests/flakes.sh b/tests/flakes.sh
index 5a00d8671..63e7f8e87 100644
--- a/tests/flakes.sh
+++ b/tests/flakes.sh
@@ -5,6 +5,11 @@ if [[ -z $(type -p git) ]]; then
     exit 99
 fi
 
+if [[ -z $(type -p hg) ]]; then
+    echo "Mercurial not installed; skipping flake tests"
+    exit 99
+fi
+
 clearStore
 rm -rf $TEST_HOME/.cache $TEST_HOME/.config
 
@@ -372,7 +377,7 @@ nix flake remove flake1
 (cd $flake7Dir && nix flake init)
 git -C $flake7Dir add flake.nix
 nix flake check $flake7Dir
-git -C $flake7Dir commit -m 'Initial'
+git -C $flake7Dir commit -a -m 'Initial'
 
 # Test 'nix flake clone'.
 rm -rf $TEST_ROOT/flake1-v2
@@ -545,11 +550,6 @@ nix flake update $flake3Dir --recreate-lock-file
 [[ $(jq .inputs.flake2.inputs.flake1.locked.url $flake3Dir/flake.lock) =~ flake7 ]]
 
 # Test Mercurial flakes.
-if [[ -z $(type -p hg) ]]; then
-    echo "Git not installed; skipping Mercurial flake tests"
-    exit 99
-fi
-
 rm -rf $flake5Dir
 hg init $flake5Dir
 
@@ -571,12 +571,9 @@ hg commit --config ui.username=foobar@example.org $flake5Dir -m 'Initial commit'
 nix build -o $TEST_ROOT/result hg+file://$flake5Dir
 [[ -e $TEST_ROOT/result/hello ]]
 
-nix flake info --json hg+file://$flake5Dir | jq -e -r .revision
+(! nix flake info --json hg+file://$flake5Dir | jq -e -r .revision)
 
-# This will fail because flake.lock is not tracked by Mercurial.
-(! nix eval hg+file://$flake5Dir#expr)
-
-hg add $flake5Dir/flake.lock
+nix eval hg+file://$flake5Dir#expr
 
 nix eval hg+file://$flake5Dir#expr