diff --git a/src/runtime-rs/Makefile b/src/runtime-rs/Makefile
index f492d1d334..7d49e7b479 100644
--- a/src/runtime-rs/Makefile
+++ b/src/runtime-rs/Makefile
@@ -452,12 +452,15 @@ optimize: $(SOURCES) | show-summary show-header
 	@RUSTFLAGS="-C link-arg=-s $(EXTRA_RUSTFLAGS) --deny warnings" cargo build --target $(TRIPLE) --$(BUILD_TYPE) $(EXTRA_RUSTFEATURES)
 
 ##TARGET clean: clean build
-clean:
+clean: clean-generated-files
 	@cargo clean
-	@rm -f $(GENERATED_FILES)
 	@rm -f tarpaulin-report.html
 	@rm -f $(CONFIGS)
 
+##TARGET clean-generated-files: clean generated files
+clean-generated-files:
+	@rm -f $(GENERATED_FILES)
+
 vendor:
 	@cargo vendor
 
diff --git a/src/runtime/Makefile b/src/runtime/Makefile
index c9cf7ac584..2d96cd3baa 100644
--- a/src/runtime/Makefile
+++ b/src/runtime/Makefile
@@ -879,15 +879,16 @@ vendor: handle_vendor
 
 static-checks-build: $(GENERATED_FILES)
 
-clean:
+clean: clean-generated-files
 	$(QUIET_CLEAN)rm -f \
-		$(CONFIGS) \
-		$(GENERATED_FILES) \
 		$(MONITOR) \
 		$(SHIMV2) \
 		$(TARGET) \
 		.git-commit .git-commit.tmp
 
+clean-generated-files:
+	$(QUIET_CLEAN)rm -f $(GENERATED_FILES)
+
 show-usage: show-header
 	@printf "• Overview:\n"
 	@printf "\n"
@@ -904,6 +905,7 @@ show-usage: show-header
 	@printf "\tfast-test                  : run tests with failfast option.\n"
 	@printf "\tcheck                      : run code checks.\n"
 	@printf "\tclean                      : remove built files.\n"
+	@printf "\tclean-generated-files      : remove generated files.\n"
 	@printf "\tcontainerd-shim-v2         : only build containerd shim v2.\n"
 	@printf "\tcoverage                   : run coverage tests.\n"
 	@printf "\tdefault                    : same as 'make build' (or just 'make').\n"
diff --git a/tools/packaging/static-build/shim-v2/build.sh b/tools/packaging/static-build/shim-v2/build.sh
index 8fc2f7bea6..f37cb91f40 100755
--- a/tools/packaging/static-build/shim-v2/build.sh
+++ b/tools/packaging/static-build/shim-v2/build.sh
@@ -62,7 +62,8 @@ sudo docker run --rm -i -v "${repo_root_dir}:${repo_root_dir}" \
 	--env CC="${CC}" \
 	-w "${repo_root_dir}/src/runtime-rs" \
 	"${container_image}" \
-	bash -c "git config --global --add safe.directory ${repo_root_dir} && make PREFIX=${PREFIX} QEMUCMD=qemu-system-${arch}"
+	bash -c "git config --global --add safe.directory ${repo_root_dir} && \
+		make clean-generated-files && make PREFIX=${PREFIX} QEMUCMD=qemu-system-${arch}"
 
 sudo docker run --rm -i -v "${repo_root_dir}:${repo_root_dir}" \
 	--env CROSS_BUILD=${CROSS_BUILD} \
@@ -77,7 +78,8 @@ sudo docker run --rm -i -v "${repo_root_dir}:${repo_root_dir}" \
 sudo docker run --rm -i -v "${repo_root_dir}:${repo_root_dir}" \
 	-w "${repo_root_dir}/src/runtime" \
 	"${container_image}" \
-	bash -c "git config --global --add safe.directory ${repo_root_dir} && make PREFIX=${PREFIX} QEMUCMD=qemu-system-${arch} ${EXTRA_OPTS}"
+	bash -c "git config --global --add safe.directory ${repo_root_dir} && \
+		make clean-generated-files && make PREFIX=${PREFIX} QEMUCMD=qemu-system-${arch} ${EXTRA_OPTS}"
 
 sudo docker run --rm -i -v "${repo_root_dir}:${repo_root_dir}" \
 	-w "${repo_root_dir}/src/runtime" \