diff --git a/Nmakefile b/Nmakefile
index f68c821101..065d24a757 100644
--- a/Nmakefile
+++ b/Nmakefile
@@ -150,8 +150,15 @@ factor.com: $(EXE_OBJS) $(DLL_OBJS)
 factor.exe: $(EXE_OBJS) $(DLL_OBJS)
 	link $(LINK_FLAGS) /out:factor.exe /SUBSYSTEM:$(SUBSYSTEM_EXE_FLAGS) $(EXE_OBJS) $(DLL_OBJS)
 
+# If we compile factor.exe, run mt.exe, and run factor.exe,
+# then Windows caches the manifest. Even on a recompile without applying
+# the mt.exe tool, if the factor.exe.manifest file is present, the manifest
+# is applied. To avoid this, we delete the .manifest file on clean
+# and copy it from a reference file on compilation and mt.exe.
+#
 factor.exe.manifest: factor.exe
-	mt -manifest factor.exe.manifest -outputresource:factor.exe;#1
+	copy factor.exe.manifest.in factor.exe.manifest
+	mt -manifest factor.exe.manifest -outputresource:"factor.exe;#1"
 
 all: factor.com factor.exe factor.dll.lib libfactor-ffi-test.dll
 
@@ -184,12 +191,15 @@ clean:
 	if exist factor.lib del factor.lib
 	if exist factor.com del factor.com
 	if exist factor.exe del factor.exe
+	if exist factor.exe.manifest del factor.exe.manifest
+	if exist factor.exp del factor.exp
 	if exist factor.dll del factor.dll
 	if exist factor.dll.lib del factor.dll.lib
+	if exist factor.dll.exp del factor.dll.exp
 	if exist libfactor-ffi-test.dll del libfactor-ffi-test.dll
 	if exist libfactor-ffi-test.exp del libfactor-ffi-test.exp
 	if exist libfactor-ffi-test.lib del libfactor-ffi-test.lib
 
-.PHONY: all default x86-32 x86-64 x86-32-vista x86-64-vista clean
+.PHONY: all default x86-32 x86-64 x86-32-vista x86-64-vista clean factor.exe.manifest
 
 .SUFFIXES: .rs
diff --git a/factor.exe.manifest b/factor.exe.manifest.in
similarity index 100%
rename from factor.exe.manifest
rename to factor.exe.manifest.in