diff --git a/tests/bootstrap_test.sh b/tests/bootstrap_test.sh
index 1258684..9342d75 100755
--- a/tests/bootstrap_test.sh
+++ b/tests/bootstrap_test.sh
@@ -144,7 +144,7 @@
   run_soong
   local ninja_mtime1=$(stat -c "%y" out/soong/build.ninja)
 
-  local glob_deps_file=out/soong/.primary/globs/0.d
+  local glob_deps_file=out/soong/.bootstrap/globs/0.d
 
   if [ -e "$glob_deps_file" ]; then
     fail "Glob deps file unexpectedly written on first build"
@@ -526,18 +526,14 @@
   [[ -e out/soong/workspace ]] || fail "Bazel workspace not created"
 }
 
-function test_bp2build_generates_fake_ninja_file {
+function test_bp2build_generates_marker_file {
   setup
   create_mock_bazel
 
   run_bp2build
 
-  if [[ ! -f "./out/soong/build.ninja" ]]; then
-    fail "./out/soong/build.ninja was not generated"
-  fi
-
-  if ! grep "build nothing: phony" "./out/soong/build.ninja"; then
-    fail "missing phony nothing target in out/soong/build.ninja"
+  if [[ ! -f "./out/soong/.bootstrap/bp2build_workspace_marker" ]]; then
+    fail "Marker file was not generated"
   fi
 }
 
@@ -577,10 +573,10 @@
   setup
 
   GENERATE_BAZEL_FILES=1 run_soong
-  local mtime1=$(stat -c "%y" out/soong/build.ninja)
+  local mtime1=$(stat -c "%y" out/soong/.bootstrap/bp2build_workspace_marker)
 
   GENERATE_BAZEL_FILES=1 run_soong
-  local mtime2=$(stat -c "%y" out/soong/build.ninja)
+  local mtime2=$(stat -c "%y" out/soong/.bootstrap/bp2build_workspace_marker)
 
   if [[ "$mtime1" != "$mtime2" ]]; then
     fail "Output Ninja file changed on null build"
@@ -712,6 +708,41 @@
   grep -q "b/${GENERATED_BUILD_FILE_NAME}' exist" "$MOCK_TOP/errors" || fail "Error for b/${GENERATED_BUILD_FILE_NAME} not found"
 }
 
+function test_bp2build_back_and_forth_null_build {
+  setup
+
+  run_soong
+  local output_mtime1=$(stat -c "%y" out/soong/build.ninja)
+
+  GENERATE_BAZEL_FILES=1 run_soong
+  local output_mtime2=$(stat -c "%y" out/soong/build.ninja)
+  if [[ "$output_mtime1" != "$output_mtime2" ]]; then
+    fail "Output Ninja file changed when switching to bp2build"
+  fi
+
+  local marker_mtime1=$(stat -c "%y" out/soong/.bootstrap/bp2build_workspace_marker)
+
+  run_soong
+  local output_mtime3=$(stat -c "%y" out/soong/build.ninja)
+  local marker_mtime2=$(stat -c "%y" out/soong/.bootstrap/bp2build_workspace_marker)
+  if [[ "$output_mtime1" != "$output_mtime3" ]]; then
+    fail "Output Ninja file changed when switching to regular build from bp2build"
+  fi
+  if [[ "$marker_mtime1" != "$marker_mtime2" ]]; then
+    fail "bp2build marker file changed when switching to regular build from bp2build"
+  fi
+
+  GENERATE_BAZEL_FILES=1 run_soong
+  local output_mtime4=$(stat -c "%y" out/soong/build.ninja)
+  local marker_mtime3=$(stat -c "%y" out/soong/.bootstrap/bp2build_workspace_marker)
+  if [[ "$output_mtime1" != "$output_mtime4" ]]; then
+    fail "Output Ninja file changed when switching back to bp2build"
+  fi
+  if [[ "$marker_mtime1" != "$marker_mtime3" ]]; then
+    fail "bp2build marker file changed when switching back to bp2build"
+  fi
+}
+
 test_smoke
 test_null_build
 test_null_build_after_docs
@@ -727,8 +758,9 @@
 test_dump_json_module_graph
 test_write_to_source_tree
 test_bp2build_smoke
-test_bp2build_generates_fake_ninja_file
+test_bp2build_generates_marker_file
 test_bp2build_null_build
+test_bp2build_back_and_forth_null_build
 test_bp2build_add_android_bp
 test_bp2build_add_to_glob
 test_bp2build_bazel_workspace_structure