diff --git a/src/libexpr/eval.cc b/src/libexpr/eval.cc
index fcfee2d29..18b8c2f91 100644
--- a/src/libexpr/eval.cc
+++ b/src/libexpr/eval.cc
@@ -304,7 +304,7 @@ EvalState::EvalState(
 
             /* Apply access control if needed. */
             if (settings.restrictEval || settings.pureEval)
-                accessor = AllowListSourceAccessor::create(accessor, {},
+                accessor = AllowListSourceAccessor::create(accessor, {}, {},
                     [&settings](const CanonPath & path) -> RestrictedPathError {
                         auto modeInformation = settings.pureEval
                             ? "in pure evaluation mode (use '--impure' to override)"
diff --git a/src/libfetchers/filtering-source-accessor.cc b/src/libfetchers/filtering-source-accessor.cc
index d4557b6d4..c6a00faef 100644
--- a/src/libfetchers/filtering-source-accessor.cc
+++ b/src/libfetchers/filtering-source-accessor.cc
@@ -58,18 +58,23 @@ void FilteringSourceAccessor::checkAccess(const CanonPath & path)
 struct AllowListSourceAccessorImpl : AllowListSourceAccessor
 {
     std::set<CanonPath> allowedPrefixes;
+    std::unordered_set<CanonPath> allowedPaths;
 
     AllowListSourceAccessorImpl(
         ref<SourceAccessor> next,
         std::set<CanonPath> && allowedPrefixes,
+        std::unordered_set<CanonPath> && allowedPaths,
         MakeNotAllowedError && makeNotAllowedError)
         : AllowListSourceAccessor(SourcePath(next), std::move(makeNotAllowedError))
         , allowedPrefixes(std::move(allowedPrefixes))
+        , allowedPaths(std::move(allowedPaths))
     { }
 
     bool isAllowed(const CanonPath & path) override
     {
-        return path.isAllowed(allowedPrefixes);
+        return
+            allowedPaths.contains(path)
+            || path.isAllowed(allowedPrefixes);
     }
 
     void allowPrefix(CanonPath prefix) override
@@ -81,9 +86,14 @@ struct AllowListSourceAccessorImpl : AllowListSourceAccessor
 ref<AllowListSourceAccessor> AllowListSourceAccessor::create(
     ref<SourceAccessor> next,
     std::set<CanonPath> && allowedPrefixes,
+    std::unordered_set<CanonPath> && allowedPaths,
     MakeNotAllowedError && makeNotAllowedError)
 {
-    return make_ref<AllowListSourceAccessorImpl>(next, std::move(allowedPrefixes), std::move(makeNotAllowedError));
+    return make_ref<AllowListSourceAccessorImpl>(
+        next,
+        std::move(allowedPrefixes),
+        std::move(allowedPaths),
+        std::move(makeNotAllowedError));
 }
 
 bool CachingFilteringSourceAccessor::isAllowed(const CanonPath & path)
diff --git a/src/libfetchers/filtering-source-accessor.hh b/src/libfetchers/filtering-source-accessor.hh
index 1f8d84e53..41889cfd7 100644
--- a/src/libfetchers/filtering-source-accessor.hh
+++ b/src/libfetchers/filtering-source-accessor.hh
@@ -2,6 +2,8 @@
 
 #include "source-path.hh"
 
+#include <unordered_set>
+
 namespace nix {
 
 /**
@@ -70,6 +72,7 @@ struct AllowListSourceAccessor : public FilteringSourceAccessor
     static ref<AllowListSourceAccessor> create(
         ref<SourceAccessor> next,
         std::set<CanonPath> && allowedPrefixes,
+        std::unordered_set<CanonPath> && allowedPaths,
         MakeNotAllowedError && makeNotAllowedError);
 
     using FilteringSourceAccessor::FilteringSourceAccessor;
diff --git a/src/libfetchers/git-utils.cc b/src/libfetchers/git-utils.cc
index 6b9d1bce6..6fa33e130 100644
--- a/src/libfetchers/git-utils.cc
+++ b/src/libfetchers/git-utils.cc
@@ -1215,20 +1215,12 @@ ref<SourceAccessor> GitRepoImpl::getAccessor(
 ref<SourceAccessor> GitRepoImpl::getAccessor(const WorkdirInfo & wd, bool exportIgnore, MakeNotAllowedError makeNotAllowedError)
 {
     auto self = ref<GitRepoImpl>(shared_from_this());
-    /* In case of an empty workdir, return an empty in-memory tree. We
-       cannot use AllowListSourceAccessor because it would return an
-       error for the root (and we can't add the root to the allow-list
-       since that would allow access to all its children). */
     ref<SourceAccessor> fileAccessor =
-        wd.files.empty()
-        ? ({
-            auto empty = makeEmptySourceAccessor();
-            empty->setPathDisplay(path.string());
-            empty;
-          })
-        : AllowListSourceAccessor::create(
+        AllowListSourceAccessor::create(
             makeFSSourceAccessor(path),
-            std::set<CanonPath> { wd.files },
+            std::set<CanonPath>{ wd.files },
+            // Always allow access to the root, but not its children.
+            std::unordered_set<CanonPath>{CanonPath::root},
             std::move(makeNotAllowedError)).cast<SourceAccessor>();
     if (exportIgnore)
         fileAccessor = make_ref<GitExportIgnoreSourceAccessor>(self, fileAccessor, std::nullopt);
diff --git a/tests/functional/flakes/source-paths.sh b/tests/functional/flakes/source-paths.sh
index a3ebf4e3a..1eb8d618d 100644
--- a/tests/functional/flakes/source-paths.sh
+++ b/tests/functional/flakes/source-paths.sh
@@ -17,7 +17,7 @@ cat > "$repo/flake.nix" <<EOF
 }
 EOF
 
-expectStderr 1 nix eval "$repo#x" | grepQuiet "error: path '$repo/flake.nix' does not exist"
+expectStderr 1 nix eval "$repo#x" | grepQuiet "error: File 'flake.nix' in the repository \"$repo\" is not tracked by Git."
 
 git -C "$repo" add flake.nix