diff --git a/doc/manual/rl-next/outpath-and-sourceinfo-fixes.md b/doc/manual/rl-next/outpath-and-sourceinfo-fixes.md
new file mode 100644
index 000000000..479a2f5cb
--- /dev/null
+++ b/doc/manual/rl-next/outpath-and-sourceinfo-fixes.md
@@ -0,0 +1,17 @@
+---
+synopsis: Non-flake inputs now contain a `sourceInfo` attribute
+issues: 13164
+prs: 13170
+---
+
+Flakes have always a `sourceInfo` attribute which describes the source of the flake.
+The `sourceInfo.outPath` is often identical to the flake's `outPath`, however it can differ when the flake is located in a subdirectory of its source.
+
+Non-flake inputs (i.e. inputs with `flake = false`) can also be located at some path _within_ a wider source.
+This usually happens when defining a relative path input within the same source as the parent flake, e.g. `inputs.foo.url = ./some-file.nix`.
+Such relative inputs will now inherit their parent's `sourceInfo`.
+
+This also means it is now possible to use `?dir=subdir` on non-flake inputs.
+
+This iterates on the work done in 2.26 to improve relative path support ([#10089](https://github.com/NixOS/nix/pull/10089)),
+and resolves a regression introduced in 2.28 relating to nested relative path inputs ([#13164](https://github.com/NixOS/nix/issues/13164)).
diff --git a/src/libflake/call-flake.nix b/src/libflake/call-flake.nix
index fe326291f..ed7947e06 100644
--- a/src/libflake/call-flake.nix
+++ b/src/libflake/call-flake.nix
@@ -39,24 +39,16 @@ let
   allNodes = mapAttrs (
     key: node:
     let
+      hasOverride = overrides ? ${key};
+      isRelative = node.locked.type or null == "path" && builtins.substring 0 1 node.locked.path != "/";
 
       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 ? ${key} then
+        if hasOverride then
           overrides.${key}.sourceInfo
-        else if node.locked.type == "path" && builtins.substring 0 1 node.locked.path != "/" then
+        else if isRelative then
           parentNode.sourceInfo
-          // {
-            outPath = parentNode.sourceInfo.outPath + ("/" + flakeDir);
-          }
         else
           # FIXME: remove obsolete node.info.
           # Note: lock file entries are always final.
@@ -64,7 +56,11 @@ let
 
       subdir = overrides.${key}.dir or node.locked.dir or "";
 
-      outPath = sourceInfo + ((if subdir == "" then "" else "/") + subdir);
+      outPath =
+        if !hasOverride && isRelative then
+          parentNode.outPath + (if node.locked.path == "" then "" else "/" + node.locked.path)
+        else
+          sourceInfo.outPath + (if subdir == "" then "" else "/" + subdir);
 
       flake = import (outPath + "/flake.nix");
 
@@ -99,9 +95,9 @@ let
           assert builtins.isFunction flake.outputs;
           result
         else
-          sourceInfo;
+          sourceInfo // { inherit sourceInfo outPath; };
 
-      inherit flakeDir sourceInfo;
+      inherit outPath sourceInfo;
     }
   ) lockFile.nodes;
 
diff --git a/tests/functional/flakes/non-flake-inputs.sh b/tests/functional/flakes/non-flake-inputs.sh
index f5e12cd01..05e656042 100644
--- a/tests/functional/flakes/non-flake-inputs.sh
+++ b/tests/functional/flakes/non-flake-inputs.sh
@@ -37,11 +37,20 @@ cat > "$flake3Dir/flake.nix" <<EOF
       url = "$nonFlakeDir/README.md";
       flake = false;
     };
+    nonFlakeFile3 = {
+      url = "$nonFlakeDir?dir=README.md";
+      flake = false;
+    };
+    relativeNonFlakeFile = {
+      url = ./config.nix;
+      flake = false;
+    };
   };
 
   description = "Fnord";
 
   outputs = inputs: rec {
+    inherit inputs;
     packages.$system.xyzzy = inputs.flake2.packages.$system.bar;
     packages.$system.sth = inputs.flake1.packages.$system.foo;
     packages.$system.fnord =
@@ -88,6 +97,43 @@ mv "$flake2Dir.tmp" "$flake2Dir"
 mv "$nonFlakeDir.tmp" "$nonFlakeDir"
 nix build -o "$TEST_ROOT/result" flake3#xyzzy flake3#fnord
 
+# Check non-flake inputs have a sourceInfo and an outPath
+#
+# This may look redundant, but the other checks below happen in a command
+# substitution subshell, so failures there will not exit this shell
+nix eval --raw flake3#inputs.nonFlake.outPath
+nix eval --raw flake3#inputs.nonFlake.sourceInfo.outPath
+nix eval --raw flake3#inputs.nonFlakeFile.outPath
+nix eval --raw flake3#inputs.nonFlakeFile.sourceInfo.outPath
+nix eval --raw flake3#inputs.nonFlakeFile2.outPath
+nix eval --raw flake3#inputs.nonFlakeFile2.sourceInfo.outPath
+nix eval --raw flake3#inputs.nonFlakeFile3.outPath
+nix eval --raw flake3#inputs.nonFlakeFile3.sourceInfo.outPath
+nix eval --raw flake3#inputs.relativeNonFlakeFile.outPath
+nix eval --raw flake3#inputs.relativeNonFlakeFile.sourceInfo.outPath
+
+# Check non-flake file inputs have the expected outPaths
+[[
+  $(nix eval --raw flake3#inputs.nonFlake.outPath) \
+  = $(nix eval --raw flake3#inputs.nonFlake.sourceInfo.outPath)
+]]
+[[
+  $(nix eval --raw flake3#inputs.nonFlakeFile.outPath) \
+  = $(nix eval --raw flake3#inputs.nonFlakeFile.sourceInfo.outPath)
+]]
+[[
+  $(nix eval --raw flake3#inputs.nonFlakeFile2.outPath) \
+  = $(nix eval --raw flake3#inputs.nonFlakeFile2.sourceInfo.outPath)
+]]
+[[
+  $(nix eval --raw flake3#inputs.nonFlakeFile3.outPath) \
+  = $(nix eval --raw flake3#inputs.nonFlakeFile3.sourceInfo.outPath)/README.md
+]]
+[[
+  $(nix eval --raw flake3#inputs.relativeNonFlakeFile.outPath) \
+  = $(nix eval --raw flake3#inputs.relativeNonFlakeFile.sourceInfo.outPath)/config.nix
+]]
+
 # Make branch "removeXyzzy" where flake3 doesn't have xyzzy anymore
 git -C "$flake3Dir" checkout -b removeXyzzy
 rm "$flake3Dir/flake.nix"
diff --git a/tests/functional/flakes/relative-paths.sh b/tests/functional/flakes/relative-paths.sh
index 9d31da0ad..5810fdebe 100644
--- a/tests/functional/flakes/relative-paths.sh
+++ b/tests/functional/flakes/relative-paths.sh
@@ -131,3 +131,46 @@ EOF
   # would fail:
   nix eval .#ok
 )
+
+# https://github.com/NixOS/nix/issues/13164
+mkdir -p "$TEST_ROOT/issue-13164/nested-flake1/nested-flake2"
+(
+  cd "$TEST_ROOT/issue-13164"
+  git init
+  git config --global user.email "you@example.com"
+  git config --global user.name "Your Name"
+  cat >flake.nix <<EOF
+{
+  inputs.nestedFlake1.url = "path:./nested-flake1";
+  outputs = { self, nestedFlake1 }: {
+    inherit nestedFlake1;
+  };
+}
+EOF
+
+  cat >nested-flake1/flake.nix <<EOF
+{
+  inputs.nestedFlake2.url = "path:./nested-flake2";
+
+  outputs = { self, nestedFlake2 }: {
+    name = "nestedFlake1";
+    inherit nestedFlake2;
+  };
+}
+EOF
+
+  cat >nested-flake1/nested-flake2/flake.nix <<EOF
+{
+  outputs = { self }: {
+    name = "nestedFlake2";
+  };
+}
+EOF
+
+  git add .
+  git commit -m "Initial commit"
+
+  # I don't understand why two calls are necessary to reproduce the issue.
+  nix eval --json .#nestedFlake1.nestedFlake2 --no-eval-cache
+  nix eval --json .#nestedFlake1.nestedFlake2 --no-eval-cache
+)