diff --git a/src/libcmd/common-eval-args.cc b/src/libcmd/common-eval-args.cc
index de967e3fe..adf816494 100644
--- a/src/libcmd/common-eval-args.cc
+++ b/src/libcmd/common-eval-args.cc
@@ -34,7 +34,9 @@ EvalSettings evalSettings {
                 // FIXME `parseFlakeRef` should take a `std::string_view`.
                 auto flakeRef = parseFlakeRef(fetchSettings, std::string { rest }, {}, true, false);
                 debug("fetching flake search path element '%s''", rest);
-                auto storePath = flakeRef.resolve(state.store).fetchTree(state.store).first;
+                auto [accessor, lockedRef] = flakeRef.resolve(state.store).lazyFetch(state.store);
+                auto storePath = nix::fetchToStore(*state.store, SourcePath(accessor), FetchMode::Copy, lockedRef.input.getName());
+                state.allowPath(storePath);
                 return state.rootPath(state.store->toRealPath(storePath));
             },
         },
@@ -183,7 +185,9 @@ SourcePath lookupFileArg(EvalState & state, std::string_view s, const Path * bas
     else if (hasPrefix(s, "flake:")) {
         experimentalFeatureSettings.require(Xp::Flakes);
         auto flakeRef = parseFlakeRef(fetchSettings, std::string(s.substr(6)), {}, true, false);
-        auto storePath = flakeRef.resolve(state.store).fetchTree(state.store).first;
+        auto [accessor, lockedRef] = flakeRef.resolve(state.store).lazyFetch(state.store);
+        auto storePath = nix::fetchToStore(*state.store, SourcePath(accessor), FetchMode::Copy, lockedRef.input.getName());
+        state.allowPath(storePath);
         return state.rootPath(CanonPath(state.store->toRealPath(storePath)));
     }
 
diff --git a/src/libflake/flake/flakeref.cc b/src/libflake/flake/flakeref.cc
index cc9403ceb..4fc720eb5 100644
--- a/src/libflake/flake/flakeref.cc
+++ b/src/libflake/flake/flakeref.cc
@@ -283,12 +283,6 @@ FlakeRef FlakeRef::fromAttrs(
         fetchers::maybeGetStrAttr(attrs, "dir").value_or(""));
 }
 
-std::pair<StorePath, FlakeRef> FlakeRef::fetchTree(ref<Store> store) const
-{
-    auto [storePath, lockedInput] = input.fetchToStore(store);
-    return {std::move(storePath), FlakeRef(std::move(lockedInput), subdir)};
-}
-
 std::pair<ref<SourceAccessor>, FlakeRef> FlakeRef::lazyFetch(ref<Store> store) const
 {
     auto [accessor, lockedInput] = input.getAccessor(store);
diff --git a/src/libflake/flake/flakeref.hh b/src/libflake/flake/flakeref.hh
index f47730da5..d3c15018e 100644
--- a/src/libflake/flake/flakeref.hh
+++ b/src/libflake/flake/flakeref.hh
@@ -71,9 +71,6 @@ struct FlakeRef
         const fetchers::Settings & fetchSettings,
         const fetchers::Attrs & attrs);
 
-    // FIXME: remove
-    std::pair<StorePath, FlakeRef> fetchTree(ref<Store> store) const;
-
     std::pair<ref<SourceAccessor>, FlakeRef> lazyFetch(ref<Store> store) const;
 };
 
diff --git a/src/nix/flake.cc b/src/nix/flake.cc
index adf391b97..6f220b495 100644
--- a/src/nix/flake.cc
+++ b/src/nix/flake.cc
@@ -17,6 +17,7 @@
 #include "eval-cache.hh"
 #include "markdown.hh"
 #include "users.hh"
+#include "fetch-to-store.hh"
 
 #include <filesystem>
 #include <nlohmann/json.hpp>
@@ -1449,7 +1450,8 @@ struct CmdFlakePrefetch : FlakeCommand, MixJSON
     {
         auto originalRef = getFlakeRef();
         auto resolvedRef = originalRef.resolve(store);
-        auto [storePath, lockedRef] = resolvedRef.fetchTree(store);
+        auto [accessor, lockedRef] = resolvedRef.lazyFetch(store);
+        auto storePath = fetchToStore(*store, accessor, FetchMode::Copy, lockedRef.input.getName());
         auto hash = store->queryPathInfo(storePath)->narHash;
 
         if (json) {