diff --git a/src/libexpr/flake/flake.cc b/src/libexpr/flake/flake.cc
index bca473453..4a781beb8 100644
--- a/src/libexpr/flake/flake.cc
+++ b/src/libexpr/flake/flake.cc
@@ -10,6 +10,7 @@
 #include "finally.hh"
 #include "fetch-settings.hh"
 #include "value-to-json.hh"
+#include "local-fs-store.hh"
 
 namespace nix {
 
@@ -755,7 +756,17 @@ void callFlake(EvalState & state,
 
         auto lockedNode = node.dynamic_pointer_cast<const LockedNode>();
 
-        auto [storePath, subdir] = state.store->toStorePath(sourcePath.path.abs());
+        // FIXME: This is a hack to support chroot stores. Remove this
+        // once we can pass a sourcePath rather than a storePath to
+        // call-flake.nix.
+        auto path = sourcePath.path.abs();
+        if (auto store = state.store.dynamic_pointer_cast<LocalFSStore>()) {
+            auto realStoreDir = store->getRealStoreDir();
+            if (isInDir(path, realStoreDir))
+                path = store->storeDir + path.substr(realStoreDir.size());
+        }
+
+        auto [storePath, subdir] = state.store->toStorePath(path);
 
         emitTreeAttrs(
             state,
diff --git a/tests/functional/chroot-store.sh b/tests/functional/chroot-store.sh
new file mode 100644
index 000000000..9e589d04b
--- /dev/null
+++ b/tests/functional/chroot-store.sh
@@ -0,0 +1,45 @@
+source common.sh
+
+echo example > $TEST_ROOT/example.txt
+mkdir -p $TEST_ROOT/x
+
+export NIX_STORE_DIR=/nix2/store
+
+CORRECT_PATH=$(cd $TEST_ROOT && nix-store --store ./x --add example.txt)
+
+[[ $CORRECT_PATH =~ ^/nix2/store/.*-example.txt$ ]]
+
+PATH1=$(cd $TEST_ROOT && nix path-info --store ./x $CORRECT_PATH)
+[ $CORRECT_PATH == $PATH1 ]
+
+PATH2=$(nix path-info --store "$TEST_ROOT/x" $CORRECT_PATH)
+[ $CORRECT_PATH == $PATH2 ]
+
+PATH3=$(nix path-info --store "local?root=$TEST_ROOT/x" $CORRECT_PATH)
+[ $CORRECT_PATH == $PATH3 ]
+
+# Ensure store info trusted works with local store
+nix --store $TEST_ROOT/x store info --json | jq -e '.trusted'
+
+# Test building in a chroot store.
+if canUseSandbox; then
+
+    flakeDir=$TEST_ROOT/flake
+    mkdir -p $flakeDir
+
+    cat > $flakeDir/flake.nix <<EOF
+{
+  outputs = inputs: rec {
+    packages.$system.default = import ./simple.nix;
+  };
+}
+EOF
+
+    cp simple.nix shell.nix simple.builder.sh config.nix $flakeDir/
+
+    outPath=$(nix build --print-out-paths --no-link --sandbox-paths '/nix? /bin? /lib? /lib64? /usr?' --store $TEST_ROOT/x path:$flakeDir)
+
+    [[ $outPath =~ ^/nix2/store/.*-simple$ ]]
+
+    [[ $(cat $TEST_ROOT/x/nix/store/$(basename $outPath)/hello) = 'Hello World!' ]]
+fi
diff --git a/tests/functional/local-store.sh b/tests/functional/local-store.sh
deleted file mode 100644
index f7c8eb3f1..000000000
--- a/tests/functional/local-store.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-source common.sh
-
-cd $TEST_ROOT
-
-echo example > example.txt
-mkdir -p ./x
-
-NIX_STORE_DIR=$TEST_ROOT/x
-
-CORRECT_PATH=$(nix-store --store ./x --add example.txt)
-
-PATH1=$(nix path-info --store ./x $CORRECT_PATH)
-[ $CORRECT_PATH == $PATH1 ]
-
-PATH2=$(nix path-info --store "$PWD/x" $CORRECT_PATH)
-[ $CORRECT_PATH == $PATH2 ]
-
-PATH3=$(nix path-info --store "local?root=$PWD/x" $CORRECT_PATH)
-[ $CORRECT_PATH == $PATH3 ]
-
-# Ensure store info trusted works with local store
-nix --store ./x store info --json | jq -e '.trusted'
diff --git a/tests/functional/local.mk b/tests/functional/local.mk
index 8bb8e3600..ca9837d32 100644
--- a/tests/functional/local.mk
+++ b/tests/functional/local.mk
@@ -83,7 +83,7 @@ nix_tests = \
   export.sh \
   config.sh \
   add.sh \
-  local-store.sh \
+  chroot-store.sh \
   filter-source.sh \
   misc.sh \
   dump-db.sh \