diff --git a/config.mak.uname b/config.mak.uname
index 911c7c0b7e..e21aa7382b 100644
--- a/config.mak.uname
+++ b/config.mak.uname
@@ -503,12 +503,11 @@ ifneq (,$(findstring MINGW,$(uname_S)))
 	NO_POSIX_GOODIES = UnfortunatelyYes
 	DEFAULT_HELP_FORMAT = html
 	NO_D_INO_IN_DIRENT = YesPlease
-	COMPAT_CFLAGS += -D__USE_MINGW_ACCESS -D_USE_32BIT_TIME_T -DNOGDI -Icompat -Icompat/win32
+	COMPAT_CFLAGS += -D__USE_MINGW_ACCESS -DNOGDI -Icompat -Icompat/win32
 	COMPAT_CFLAGS += -DSTRIP_EXTENSION=\".exe\"
 	COMPAT_OBJS += compat/mingw.o compat/winansi.o \
 		compat/win32/pthread.o compat/win32/syslog.o \
 		compat/win32/dirent.o compat/win32/fscache.o
-	BASIC_LDFLAGS += -Wl,--large-address-aware
 	EXTLIBS += -lws2_32
 	GITLIBS += git.res
 	PTHREAD_LIBS =
@@ -530,9 +529,20 @@ else
 	NO_CURL = YesPlease
 endif
 ifeq (MINGW32,$(MSYSTEM))
+	prefix = /mingw32/
+endif
+ifeq (MINGW64,$(MSYSTEM))
+	prefix = /mingw64/
+else
+	COMPAT_CFLAGS += -D_USE_32BIT_TIME_T
+	BASIC_LDFLAGS += -Wl,--large-address-aware
+endif
+ifeq (MSYS,$(MSYSTEM))
+	prefix = /usr/
+endif
+ifneq (,$(MSYSTEM))
 	CC = gcc
 	htmldir = share/doc/git/$(firstword $(subst -, ,$(GIT_VERSION)))/html
-	prefix = /mingw32/
 	INSTALL = /bin/install
 	NO_R_TO_GCC_LINKER = YesPlease
 	INTERNAL_QSORT = YesPlease