diff --git a/src/libflake/call-flake.nix b/src/libflake/call-flake.nix
index 1e9e21048..fe326291f 100644
--- a/src/libflake/call-flake.nix
+++ b/src/libflake/call-flake.nix
@@ -14,6 +14,7 @@ overrides:
 fetchTreeFinal:
 
 let
+  inherit (builtins) mapAttrs;
 
   lockFile = builtins.fromJSON lockFileStr;
 
@@ -35,19 +36,26 @@ let
         (resolveInput lockFile.nodes.${nodeName}.inputs.${builtins.head path})
         (builtins.tail path);
 
-  allNodes = builtins.mapAttrs (
+  allNodes = mapAttrs (
     key: node:
     let
 
       parentNode = allNodes.${getInputByPath lockFile.root node.parent};
 
+      flakeDir =
+        let
+          dir = overrides.${key}.dir or node.locked.path or "";
+          parentDir = parentNode.flakeDir;
+        in
+        if node ? parent then parentDir + ("/" + dir) else dir;
+
       sourceInfo =
         if overrides ? ${key} then
           overrides.${key}.sourceInfo
         else if node.locked.type == "path" && builtins.substring 0 1 node.locked.path != "/" then
           parentNode.sourceInfo
           // {
-            outPath = parentNode.outPath + ("/" + node.locked.path);
+            outPath = parentNode.sourceInfo.outPath + ("/" + flakeDir);
           }
         else
           # FIXME: remove obsolete node.info.
@@ -60,7 +68,7 @@ let
 
       flake = import (outPath + "/flake.nix");
 
-      inputs = builtins.mapAttrs (inputName: inputSpec: allNodes.${resolveInput inputSpec}) (
+      inputs = mapAttrs (inputName: inputSpec: allNodes.${resolveInput inputSpec}.result) (
         node.inputs or { }
       );
 
@@ -85,12 +93,17 @@ let
         };
 
     in
-    if node.flake or true then
-      assert builtins.isFunction flake.outputs;
-      result
-    else
-      sourceInfo
+    {
+      result =
+        if node.flake or true then
+          assert builtins.isFunction flake.outputs;
+          result
+        else
+          sourceInfo;
+
+      inherit flakeDir sourceInfo;
+    }
   ) lockFile.nodes;
 
 in
-allNodes.${lockFile.root}
+allNodes.${lockFile.root}.result
diff --git a/tests/functional/flakes/relative-paths.sh b/tests/functional/flakes/relative-paths.sh
index 3f7ca3f46..4648ba98c 100644
--- a/tests/functional/flakes/relative-paths.sh
+++ b/tests/functional/flakes/relative-paths.sh
@@ -108,3 +108,24 @@ EOF
 [[ $(nix eval "$rootFlake#z") = 90 ]]
 
 fi
+
+# https://github.com/NixOS/nix/pull/10089#discussion_r2041984987
+# https://github.com/NixOS/nix/issues/13018
+mkdir -p "$TEST_ROOT/issue-13018/example"
+(
+  cd "$TEST_ROOT/issue-13018"
+  git init
+  echo '{ outputs = _: { }; }' >flake.nix
+  cat >example/flake.nix <<EOF
+{
+  inputs.parent.url = ../.;
+  outputs = { parent, ... }: builtins.seq parent { ok = null; };
+}
+EOF
+  git add -N .
+  cd example
+  # Important: the error does not trigger for an in-memory lock!
+  nix flake lock
+  # would fail:
+  nix eval .#ok
+)