diff --git a/config.mak.uname b/config.mak.uname
index 91d9e0635a..c591b34051 100644
--- a/config.mak.uname
+++ b/config.mak.uname
@@ -438,14 +438,8 @@ ifeq ($(uname_S),Windows)
 	GIT_VERSION := $(GIT_VERSION).MSVC
 	pathsep = ;
 	# Assume that this is built in Git for Windows' SDK
-        ifeq (MINGW32,$(MSYSTEM))
-		prefix = /mingw32
-        else
-                ifeq (CLANGARM64,$(MSYSTEM))
-			prefix = /clangarm64
-                else
-			prefix = /mingw64
-                endif
+        ifneq (,$(MSYSTEM))
+		prefix = $(MINGW_PREFIX)
         endif
 	# Prepend MSVC 64-bit tool-chain to PATH.
 	#
@@ -499,7 +493,7 @@ ifeq ($(uname_S),Windows)
 	NATIVE_CRLF = YesPlease
 	DEFAULT_HELP_FORMAT = html
 	SKIP_DASHED_BUILT_INS = YabbaDabbaDoo
-ifeq (/mingw64,$(subst 32,64,$(subst clangarm,mingw,$(prefix))))
+ifneq (,$(MINGW_PREFIX))
 	# Move system config into top-level /etc/
 	ETC_GITCONFIG = ../etc/gitconfig
 	ETC_GITATTRIBUTES = ../etc/gitattributes
@@ -730,26 +724,23 @@ ifeq ($(uname_S),MINGW)
         ifneq (,$(findstring -O,$(filter-out -O0 -Og,$(CFLAGS))))
 		BASIC_LDFLAGS += -Wl,--dynamicbase
         endif
-        ifeq (MINGW32,$(MSYSTEM))
-		prefix = /mingw32
-		HOST_CPU = i686
-		BASIC_LDFLAGS += -Wl,--pic-executable,-e,_mainCRTStartup
+        ifneq (,$(MSYSTEM))
+                ifeq ($(MINGW_PREFIX),$(filter-out /%,$(MINGW_PREFIX)))
+			# Override if empty or does not start with a slash
+			MINGW_PREFIX := /$(shell echo '$(MSYSTEM)' | tr A-Z a-z)
+                endif
+		prefix = $(MINGW_PREFIX)
+		HOST_CPU = $(patsubst %-w64-mingw32,%,$(MINGW_CHOST))
+		BASIC_LDFLAGS += -Wl,--pic-executable
+		COMPAT_CFLAGS += -DDETECT_MSYS_TTY
+                ifeq (MINGW32,$(MSYSTEM))
+			BASIC_LDFLAGS += -Wl,--large-address-aware
+                endif
+		# Move system config into top-level /etc/
+		ETC_GITCONFIG = ../etc/gitconfig
+		ETC_GITATTRIBUTES = ../etc/gitattributes
         endif
-        ifeq (MINGW64,$(MSYSTEM))
-		prefix = /mingw64
-		HOST_CPU = x86_64
-		BASIC_LDFLAGS += -Wl,--pic-executable,-e,mainCRTStartup
-        else ifeq (CLANGARM64,$(MSYSTEM))
-		prefix = /clangarm64
-		HOST_CPU = aarch64
-		BASIC_LDFLAGS += -Wl,--pic-executable,-e,mainCRTStartup
-        else
-		COMPAT_CFLAGS += -D_USE_32BIT_TIME_T
-		BASIC_LDFLAGS += -Wl,--large-address-aware
-        endif
-	CC = gcc
-	COMPAT_CFLAGS += -D__USE_MINGW_ANSI_STDIO=0 -DDETECT_MSYS_TTY \
-		-fstack-protector-strong
+	COMPAT_CFLAGS += -D__USE_MINGW_ANSI_STDIO=0 -fstack-protector-strong
 	EXTLIBS += -lntdll
 	EXTRA_PROGRAMS += headless-git$X
 	INSTALL = /bin/install
@@ -759,11 +750,6 @@ ifeq ($(uname_S),MINGW)
 	USE_LIBPCRE = YesPlease
 	USE_MIMALLOC = YesPlease
 	NO_PYTHON =
-        ifeq (/mingw64,$(subst 32,64,$(subst clangarm,mingw,$(prefix))))
-		# Move system config into top-level /etc/
-		ETC_GITCONFIG = ../etc/gitconfig
-		ETC_GITATTRIBUTES = ../etc/gitattributes
-        endif
 endif
 ifeq ($(uname_S),QNX)
 	COMPAT_CFLAGS += -DSA_RESTART=0
diff --git a/contrib/buildsystems/CMakeLists.txt b/contrib/buildsystems/CMakeLists.txt
index fa3226e408..abe2e364e6 100644
--- a/contrib/buildsystems/CMakeLists.txt
+++ b/contrib/buildsystems/CMakeLists.txt
@@ -281,7 +281,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
 				_CONSOLE DETECT_MSYS_TTY STRIP_EXTENSION=".exe"  NO_SYMLINK_HEAD UNRELIABLE_FSTAT
 				NOGDI OBJECT_CREATION_MODE=1 __USE_MINGW_ANSI_STDIO=0
 				USE_NED_ALLOCATOR OVERRIDE_STRDUP MMAP_PREVENTS_DELETE USE_WIN32_MMAP
-				HAVE_WPGMPTR ENSURE_MSYSTEM_IS_SET HAVE_RTLGENRANDOM)
+				HAVE_WPGMPTR HAVE_RTLGENRANDOM)
+	if(CMAKE_GENERATOR_PLATFORM STREQUAL "x64")
+		add_compile_definitions(ENSURE_MSYSTEM_IS_SET="MINGW64" MINGW_PREFIX="mingw64")
+	elseif(CMAKE_GENERATOR_PLATFORM STREQUAL "arm64")
+		add_compile_definitions(ENSURE_MSYSTEM_IS_SET="CLANGARM64" MINGW_PREFIX="clangarm64")
+	elseif(CMAKE_GENERATOR_PLATFORM STREQUAL "x86")
+		add_compile_definitions(ENSURE_MSYSTEM_IS_SET="MINGW32" MINGW_PREFIX="mingw32")
+	endif()
 	list(APPEND compat_SOURCES
 		compat/mingw.c
 		compat/winansi.c
diff --git a/environment.c b/environment.c
index b65b85a01f..e2bffb3a34 100644
--- a/environment.c
+++ b/environment.c
@@ -91,16 +91,22 @@ int max_allowed_tree_depth =
 	 * the stack overflow can occur.
 	 */
 	512;
-#elif defined(GIT_WINDOWS_NATIVE) && defined(__clang__) && defined(__aarch64__)
+#elif defined(GIT_WINDOWS_NATIVE) && defined(__clang__)
 	/*
-	 * Similar to Visual C, it seems that on Windows/ARM64 the clang-based
-	 * builds have a smaller stack space available. When running out of
-	 * that stack space, a `STATUS_STACK_OVERFLOW` is produced. When the
+	 * Similar to Visual C, it seems that clang-based builds on Windows
+	 * have a smaller stack space available. When running out of that
+	 * stack space, a `STATUS_STACK_OVERFLOW` is produced. When the
 	 * Git command was run from an MSYS2 Bash, this unfortunately results
 	 * in an exit code 127. Let's prevent that by lowering the maximal
-	 * tree depth; This value seems to be low enough.
+	 * tree depth; Unfortunately, it seems that the exact limit differs
+	 * for aarch64 vs x86_64, and the difference is too large to simply
+	 * use a single limit.
 	 */
+#if defined(__aarch64__)
 	1280;
+#else
+	1152;
+#endif
 #else
 	2048;
 #endif
diff --git a/meson.build b/meson.build
index dd52efd1c8..e7e39045da 100644
--- a/meson.build
+++ b/meson.build
@@ -1268,7 +1268,6 @@ elif host_machine.system() == 'windows'
 
   libgit_c_args += [
     '-DDETECT_MSYS_TTY',
-    '-DENSURE_MSYSTEM_IS_SET',
     '-DNATIVE_CRLF',
     '-DNOGDI',
     '-DNO_POSIX_GOODIES',
@@ -1278,6 +1277,18 @@ elif host_machine.system() == 'windows'
     '-D__USE_MINGW_ANSI_STDIO=0',
   ]
 
+  msystem = get_option('msystem')
+  if msystem != ''
+    mingw_prefix = get_option('mingw_prefix')
+    if mingw_prefix == ''
+      mingw_prefix = '/' + msystem.to_lower()
+    endif
+    libgit_c_args += [
+      '-DENSURE_MSYSTEM_IS_SET="' + msystem + '"',
+      '-DMINGW_PREFIX="' + mingw_prefix + '"'
+    ]
+  endif
+
   libgit_dependencies += compiler.find_library('ntdll')
   libgit_include_directories += 'compat/win32'
   if compiler.get_id() == 'msvc'
diff --git a/meson_options.txt b/meson_options.txt
index e0be260ae1..c2d9f0bfc0 100644
--- a/meson_options.txt
+++ b/meson_options.txt
@@ -21,6 +21,10 @@ option('runtime_prefix', type: 'boolean', value: false,
   description: 'Resolve ancillary tooling and support files relative to the location of the runtime binary instead of hard-coding them into the binary.')
 option('sane_tool_path', type: 'array', value: [],
   description: 'An array of paths to pick up tools from in case the normal tools are broken or lacking.')
+option('msystem', type: 'string', value: '',
+  description: 'Fall-back on Windows when MSYSTEM is not set.')
+option('mingw_prefix', type: 'string', value: '',
+  description: 'Fall-back on Windows when MINGW_PREFIX is not set.')
 
 # Build information compiled into Git and other parts like documentation.
 option('build_date', type: 'string', value: '',