Are you sure you have an EFI installation of Manjaro? Aren’t you supposed to have an error with the memtest script (that I removed a while back to stop having the error while running update-grub) on a EFI install? Something’s odd here to me.
To me it looks like
the Windows EFI partition is on the second drive
Now he has got two
and needs to go through Grub on the first partition to boot either System
He probably needs to use the Windows EFI
Not sure - I never had a dual boot system with two drives and Windows partitions on both.
It seems to work ok - just not the way he want’s it to work.
By second drive , You mean nvme0n1 right? , Thats my ssd(128gb) where windows is installed. And i created 200gb partition in my hdd(1tb) where i installed manjaro(root,home,swap). and for boot/efi , when installing i clicked edit on nvme0n1’s efi system and set the mount point as boot/efi. I even tried creating a separate boot partition before in my previous installations , and all of them resulted the same(grub rescue).
when installing i clicked edit on nvme0n1’s efi system and set the mount point as boot/efi.
That didn’t seem to have worked, then.
To be sure, check how the chroot is assembled.
… where which partition actually gets mounted when you enter chroot
two terminals:
- one you will do the chroot in
- and one you use to watch what happens
use, for instance:
mount
before you enter chroot
and then again after you did
from that second terminal
it will show you what got mounted where
It should show
/dev/sda3 on /mnt
I don’t know what /dev/sda5 represents - probably /home
if that is so, it should end up at /mnt/home - but if it’s /home it is not important here
It should also show /dev/nvme0n1p1 mounted to /mnt/boot/EFI (I believe …)
I think this is what should happen but I think that this is not what actually does happen.
Compare that hypothesis to reality 
It mounted properly , i checked while chrooting manually , /mnt was in sda3 , /mnt/boot/efi was in nvme0n1p1.
Then I can’t help you to sort this out.
I’d rather not add confusion and unfounded and untested opinion.
I never had a system with two drives and it is a very long time since I had Windows.
Someone else who has actually done this and knows what he/she is talking about will hopefully help.
I can’t.
Sorry!
So , I disabled fast boot in BIOS , and its fixed. 
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