diff --git a/packages/flutter_tools/templates/app/linux.tmpl/CMakeLists.txt.tmpl b/packages/flutter_tools/templates/app/linux.tmpl/CMakeLists.txt.tmpl
index c0f6e596eaa..a1811586a3d 100644
--- a/packages/flutter_tools/templates/app/linux.tmpl/CMakeLists.txt.tmpl
+++ b/packages/flutter_tools/templates/app/linux.tmpl/CMakeLists.txt.tmpl
@@ -46,10 +46,17 @@ include(flutter/generated_plugins.cmake)
 # === Installation ===
 # By default, "installing" just makes a relocatable bundle in the build
 # directory.
+set(BUILD_BUNDLE_DIR "${PROJECT_BINARY_DIR}/bundle")
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "${PROJECT_BINARY_DIR}/bundle" CACHE PATH "..." FORCE)
+  set(CMAKE_INSTALL_PREFIX "${BUILD_BUNDLE_DIR}" CACHE PATH "..." FORCE)
 endif()
 
+# BundleUtilities doesn't re-copy changed files, so start with a clean build
+# bundle directory every time.
+INSTALL(CODE "
+  file(REMOVE_RECURSE \"${BUILD_BUNDLE_DIR}/\")
+  " COMPONENT Runtime)
+
 set(INSTALL_BUNDLE_DATA_DIR "${CMAKE_INSTALL_PREFIX}/data")
 set(INSTALL_BUNDLE_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib")