Update the system packages with pacman --needed -Sy bash pacman pacman-mirrors msys2-runtime Close MSYS2, run it again from Start menu and update the rest with pacman -Su MSYS2 shell with pacman's output about system upgrade Now Pacman is fully committed to the windows cause :)

my msys2 home has moved from a linux like one to a windows like one. How to restore it?

Changing the Windows environment variable HOME solves the problem.