diff --git a/config/Makefile.in b/config/Makefile.in
index 2cdc1c4a2e2e..9f162468de3c 100644
--- a/config/Makefile.in
+++ b/config/Makefile.in
@@ -166,6 +166,7 @@ check-preprocessor::
 check-jar-mn::
 	make -C tests/src-simple check-jar
 	make -C tests/src-simple check-flat
+	make -C tests/src-simple check-flat USE_EXTENSION_MANIFEST=1
 ifneq ($(OS_ARCH), WINNT)
 	make -C tests/src-simple check-symlink
 endif
diff --git a/config/tests/chrome.manifest.flat b/config/tests/chrome.manifest.flat
new file mode 100644
index 000000000000..4e3a144f3f9f
--- /dev/null
+++ b/config/tests/chrome.manifest.flat
@@ -0,0 +1,4 @@
+content test chrome/test/one xpcnativewrappers=no
+locale ab-X-stuff chrome/test/three
+overlay chrome://one/file.xml chrome://two/otherfile.xml
+skin test classic chrome/test/one
diff --git a/config/tests/src-simple/Makefile.in b/config/tests/src-simple/Makefile.in
index 2d75e00cce1c..5c33a50583d2 100644
--- a/config/tests/src-simple/Makefile.in
+++ b/config/tests/src-simple/Makefile.in
@@ -52,11 +52,14 @@ DEFINES += \
 	-DAB_CD=ab-X-stuff \
 	$(NULL)
 
+MY_MANIFEST = $(if $(USE_EXTENSION_MANIFEST), $(FINAL_TARGET)/chrome.manifest, $(FINAL_TARGET)/chrome/test.manifest)
+REF_MANIFEST = $(if $(USE_EXTENSION_MANIFEST),chrome.manifest,test.manifest)
+
 check-%::
 	if test -d $(FINAL_TARGET); then rm -rf $(FINAL_TARGET); fi;
 	make realchrome MOZ_CHROME_FILE_FORMAT=$*
 	@echo "Comparing manifests..."
-	@if ! sort $(FINAL_TARGET)/chrome/test.manifest | diff -u $(srcdir)/../test.manifest.$* - ; then \
+	@if ! sort $(MY_MANIFEST) | diff -u $(srcdir)/../$(REF_MANIFEST).$* - ; then \
 	  echo "FAIL: different content in manifest!" ; \
 	fi
 	@if [ $* == "jar" ]; then \