diff --git a/src/libexpr/primops/flake.cc b/src/libexpr/primops/flake.cc
index 88a0293e3..e806ef6c7 100644
--- a/src/libexpr/primops/flake.cc
+++ b/src/libexpr/primops/flake.cc
@@ -194,11 +194,8 @@ static FlakeRef lookupFlake(EvalState & state, const FlakeRef & flakeRef, const
     return flakeRef;
 }
 
-static FlakeSourceInfo fetchFlake(EvalState & state, const FlakeRef flakeRef, bool impureIsAllowed = false)
+static FlakeSourceInfo fetchFlake(EvalState & state, const FlakeRef fRef, bool impureIsAllowed = false)
 {
-    FlakeRef fRef = lookupFlake(state, flakeRef,
-        impureIsAllowed ? state.getFlakeRegistries() : std::vector<std::shared_ptr<FlakeRegistry>>());
-
     if (evalSettings.pureEval && !impureIsAllowed && !fRef.isImmutable())
         throw Error("requested to fetch mutable flake '%s' in pure mode", fRef);
 
@@ -266,26 +263,31 @@ static FlakeSourceInfo fetchFlake(EvalState & state, const FlakeRef flakeRef, bo
 // This will return the flake which corresponds to a given FlakeRef. The lookupFlake is done within this function.
 Flake getFlake(EvalState & state, const FlakeRef & flakeRef, bool impureIsAllowed = false)
 {
-    FlakeSourceInfo sourceInfo = fetchFlake(state, flakeRef, impureIsAllowed);
+    FlakeRef resolvedRef = lookupFlake(state, flakeRef,
+        impureIsAllowed ? state.getFlakeRegistries() : std::vector<std::shared_ptr<FlakeRegistry>>());
+
+    FlakeSourceInfo sourceInfo = fetchFlake(state, resolvedRef, impureIsAllowed);
     debug("got flake source '%s' with revision %s",
         sourceInfo.storePath, sourceInfo.rev.value_or(Hash(htSHA1)).to_string(Base16, false));
 
+    resolvedRef = sourceInfo.flakeRef; // `resolvedRef` is now immutable
+
     state.store->assertStorePath(sourceInfo.storePath);
 
     if (state.allowedPaths)
         state.allowedPaths->insert(sourceInfo.storePath);
 
-    Flake flake(flakeRef, std::move(sourceInfo));
-    if (std::get_if<FlakeRef::IsGitHub>(&flakeRef.data)) {
+    Flake flake(resolvedRef, std::move(sourceInfo));
+    if (std::get_if<FlakeRef::IsGitHub>(&resolvedRef.data)) {
         // FIXME: ehm?
         if (flake.sourceInfo.rev)
-            flake.ref = FlakeRef(flakeRef.baseRef().to_string()
+            flake.ref = FlakeRef(resolvedRef.baseRef().to_string()
                 + "/" + flake.sourceInfo.rev->to_string(Base16, false));
     }
 
-    Path flakeFile = sourceInfo.storePath + "/flake.nix";
+    Path flakeFile = sourceInfo.storePath + resolvedRef.subdir + "/flake.nix";
     if (!pathExists(flakeFile))
-        throw Error("source tree referenced by '%s' does not contain a 'flake.nix' file", flakeRef);
+        throw Error("source tree referenced by '%s' does not contain a 'flake.nix' file", resolvedRef);
 
     Value vInfo;
     state.evalFile(flakeFile, vInfo); // FIXME: symlink attack
diff --git a/src/libexpr/primops/flakeref.cc b/src/libexpr/primops/flakeref.cc
index b91bbee2a..022535515 100644
--- a/src/libexpr/primops/flakeref.cc
+++ b/src/libexpr/primops/flakeref.cc
@@ -139,6 +139,7 @@ std::string FlakeRef::to_string() const
 
     string += (ref ? "/" + *ref : "") +
               (rev ? "/" + rev->to_string(Base16, false) : "");
+    if (subdir != "") string += "?dir=" + subdir;
     return string;
 }
 
diff --git a/src/libexpr/primops/flakeref.hh b/src/libexpr/primops/flakeref.hh
index 51fdc3b70..299094634 100644
--- a/src/libexpr/primops/flakeref.hh
+++ b/src/libexpr/primops/flakeref.hh
@@ -69,7 +69,7 @@ namespace nix {
        https://example.org/my/repo.git
        https://example.org/my/repo.git?ref=release-1.2.3
        https://example.org/my/repo.git?rev=e72daba8250068216d79d2aeef40d4d95aff6666
-       git://github.com/edolstra/dwarffs.git\?ref=flake\&rev=2efca4bc9da70fb001b26c3dc858c6397d3c4817
+       git://github.com/edolstra/dwarffs.git?ref=flake&rev=2efca4bc9da70fb001b26c3dc858c6397d3c4817
 
    * /path.git(\?attr(&attr)*)?
 
@@ -144,17 +144,18 @@ struct FlakeRef
 
     std::optional<std::string> ref;
     std::optional<Hash> rev;
+    Path subdir = ""; // This is a relative path pointing at the flake.nix file's directory, relative to the git root.
 
     bool operator<(const FlakeRef & flakeRef) const
     {
-        return std::make_tuple(this->data, ref, rev) <
-            std::make_tuple(flakeRef.data, flakeRef.ref, flakeRef.rev);
+        return std::make_tuple(data, ref, rev, subdir) <
+            std::make_tuple(flakeRef.data, flakeRef.ref, flakeRef.rev, subdir);
     }
 
     bool operator==(const FlakeRef & flakeRef) const
     {
-        return std::make_tuple(this->data, ref, rev) ==
-            std::make_tuple(flakeRef.data, flakeRef.ref, flakeRef.rev);
+        return std::make_tuple(data, ref, rev, subdir) ==
+            std::make_tuple(flakeRef.data, flakeRef.ref, flakeRef.rev, flakeRef.subdir);
     }
 
     // Parse a flake URI.