diff --git a/config.mak.uname b/config.mak.uname
index b0592c15cc..4b2e1b807f 100644
--- a/config.mak.uname
+++ b/config.mak.uname
@@ -518,13 +518,12 @@ ifneq (,$(findstring MINGW,$(uname_S)))
 	NO_INET_NTOP = YesPlease
 	NO_POSIX_GOODIES = UnfortunatelyYes
 	DEFAULT_HELP_FORMAT = html
-	COMPAT_CFLAGS += -D_USE_32BIT_TIME_T -DNOGDI -Icompat -Icompat/win32
+	COMPAT_CFLAGS += -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
 	BASIC_CFLAGS += -DPROTECT_NTFS_DEFAULT=1
-	BASIC_LDFLAGS += -Wl,--large-address-aware
 	EXTLIBS += -lws2_32
 	GITLIBS += git.res
 	PTHREAD_LIBS =
@@ -545,8 +544,17 @@ ifneq (,$(wildcard ../THIS_IS_MSYSGIT))
 else
 	ifeq ($(shell expr "$(uname_R)" : '2\.'),2)
 		# MSys2
+		prefix = /usr/
+		ifeq (MINGW32,$(MSYSTEM))
+			prefix = /mingw32
+		endif
+		ifeq (MINGW64,$(MSYSTEM))
+			prefix = /mingw64
+		else
+			COMPAT_CFLAGS += -D_USE_32BIT_TIME_T
+			BASIC_LDFLAGS += -Wl,--large-address-aware
+		endif
 		CC = gcc
-		prefix = /mingw32
 		COMPAT_CFLAGS += -D__USE_MINGW_ANSI_STDIO=0
 		INSTALL = /bin/install
 		NO_R_TO_GCC_LINKER = YesPlease