diff --git a/git-gui/git-gui.sh b/git-gui/git-gui.sh
index 229aa9baa6d622..0da364845228f1 100755
--- a/git-gui/git-gui.sh
+++ b/git-gui/git-gui.sh
@@ -275,6 +275,10 @@ proc is_Cygwin {} {
 				set _iscygwin 0
 			} else {
 				set _iscygwin 1
+				# Handle MSys2 which is only cygwin when MSYSTEM is MSYS.
+				if {[info exists ::env(MSYSTEM)] && $::env(MSYSTEM) ne "MSYS"} {
+					set _iscygwin 0
+				}
 			}
 		} else {
 			set _iscygwin 0
diff --git a/git-gui/lib/shortcut.tcl b/git-gui/lib/shortcut.tcl
index 78878ef89d1121..39d23f96dfcab1 100644
--- a/git-gui/lib/shortcut.tcl
+++ b/git-gui/lib/shortcut.tcl
@@ -11,11 +11,14 @@ proc do_windows_shortcut {} {
 		if {[file extension $fn] ne {.lnk}} {
 			set fn ${fn}.lnk
 		}
+		# Use git-gui.exe if available (ie: git-for-windows)
+		set cmdLine [auto_execok git-gui.exe]
+		if {$cmdLine eq {}} {
+			set cmdLine [list [info nameofexecutable] \
+							 [file normalize $::argv0]]
+		}
 		if {[catch {
-				win32_create_lnk $fn [list \
-					[info nameofexecutable] \
-					[file normalize $::argv0] \
-					] \
+				win32_create_lnk $fn $cmdLine \
 					[file normalize $_gitworktree]
 			} err]} {
 			error_popup [strcat [mc "Cannot write shortcut:"] "\n\n$err"]