The problem did not seem to be the chroot but the way that I use binfmt, it is strange because the commands

mount -t binfmt_misc none /proc/sys/fs/binfmt_misc
echo ':i386:M::\x7fELF\x01\x00\x00\x00\x00\x00\x00\x00\ x00\x00\x00\x00\x02\x00\x03:\xff\xff\xff\xff\xff\x fe\xfe\xff\xff\xff\xff\xff\xff\xff\xff\xff\xfb\xff \xff:/home/user/qemu-i386:' >/proc/sys/fs/binfmt_misc/register

did not return errors.
What could be wrong here ?

Edit: wait, the command

echo ':i386:M::\x7fELF\x01\x00\x00\x00\x00\x00\x00\x00\ x00\x00\x00\x00\x02\x00\x03:\xff\xff\xff\xff\xff\x fe\xfe\xff\xff\xff\xff\xff\xff\xff\xff\xff\xfb\xff \xff:/home/user/qemu-i386:' >/proc/sys/fs/binfmt_misc/register

don't prints on stderr but returns an error code of 1
strace says:
write(1, ":i386:M::\\x7fELF\\x01\\x00\\x00\\x00"..., 179) = -1 EINVAL (Invalid argument)