Remove Fedora from a dual boot with Windows 11 on separate disks

I want to safely remove Fedora from my Laptop. On the Disk 1 (the smaller one) I carry Windows 11 and nothing else while on Disk 0 (the larger one), I carry general files and my Fedora 41 Workstation installation.

Can anyone tell me the best way to safely remove the entire Fedora system without compromising my general files or my Windows System? I’m aware of the process to remove the EFI entry but I just want to be sure I don’t mess anything up as this Laptop carries important files! Thank you in advance, great community!

Please provide the output of lsblk -f and/or sudo fdisk -l while booted to fedora.
Once we see the exact layout we can provide detailed info.

From that image it would appear that the second, third, and 4th partitions on Disk 0 may be the fedora installation but it does not tell us with any certainty.

From the size it look like you have on the 3 last partitions a typical fedora installation made with auto-install (600EFI / 1GB (/boot) / ~194GB (/,/home) )

You could test just make this 3 partitions “hidden”, while setting this flag. This is possible to do with a fedora boot live iso and the gparted app. If something goes wrong just remove the “hidden” flag and id should be as it was.

Personal HD layout for F41 installation

You might have to remove boot & esp flag from /boot/efi too on Disk0 ?!

alessio@laptop-fedora-di-alessio:~$ lsblk -f
NAME FSTYPE FSVER LABEL UUID FSAVAIL FSUSE% MOUNTPOINTS
sda
├─sda1

├─sda2
│ ntfs ALESSIO F45C2FF95C2FB570
├─sda3
│ vfat FAT32 4A79-5548 563.4M 6% /boot/efi
├─sda4
│ ext4 1.0 2524d21e-7a37-409a-ae3e-0dce0d4682af 345.3M 58% /boot
└─sda5
btrfs fedora 818e5090-b4ba-4eee-8aa0-2cf095878b76 167.5G 12% /home
/
zram0
[SWAP]
nvme0n1

├─nvme0n1p1
│ vfat FAT32 SYSTEM 2263-EB88
├─nvme0n1p2

├─nvme0n1p3
│ ntfs Windows A632051A3204F15B
└─nvme0n1p4
ntfs 924ACD794ACD5A9D

alessio@laptop-fedora-di-alessio:~$ sudo fdisk -l
[sudo] password for alessio: 
Disk /dev/sda: 931.51 GiB, 1000204886016 bytes, 1953525168 sectors
Disk model: CT1000BX500SSD1 
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 26108985-96DD-446D-827C-BB6CE9D931FC

Device          Start        End    Sectors   Size Type
/dev/sda1          34      32767      32734    16M Microsoft reserved
/dev/sda2       32768 1543921663 1543888896 736.2G Microsoft basic data
/dev/sda3  1543921664 1545150463    1228800   600M EFI System
/dev/sda4  1545150464 1547247615    2097152     1G Linux extended boot
/dev/sda5  1547247616 1953523711  406276096 193.7G Linux filesystem


Disk /dev/nvme0n1: 476.94 GiB, 512110190592 bytes, 1000215216 sectors
Disk model: SK hynix BC511 HFM512GDJTNI-82A0A       
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 364C76AC-8C3D-4CE8-88B2-8F544E7AAA34

Device             Start        End   Sectors   Size Type
/dev/nvme0n1p1      2048     534527    532480   260M EFI System
/dev/nvme0n1p2    534528     567295     32768    16M Microsoft reserved
/dev/nvme0n1p3    567296  997730303 997163008 475.5G Microsoft basic data
/dev/nvme0n1p4 997730304 1000198143   2467840   1.2G Windows recovery environment


Disk /dev/zram0: 8 GiB, 8589934592 bytes, 2097152 sectors
Units: sectors of 1 * 4096 = 4096 bytes
Sector size (logical/physical): 4096 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes

This appears to be your fedora installation.
you can boot to the live media, then install gparted and use that to remove those 3 partitions.
Once done then you could boot back to windows and make use of the space as you choose.
You may need to enter the bios setup menu and switch the boot order to boot from the windows disk.

Can I do it from the windows partition manager? Otherwise I would have to create a new media and I don’t have functioning flash USBs with me at the moment. Or is it safer to do it with gparted?

I proposed you just hide the partitions to see if your system works fine. If yes then i think it is up to you wich tools you want to use. NTFS is tipicaly a windows thing, just watchout that you not delete this by accident.

I would guess that if windows is able to manipulate those partitions it should work.

I don’t manage disks with windows and do not have win 11 so cannot be certain.

I held my breath and used MiniTool Partition Wizard, removed the three partitions and everything’s fine. It also automatically removed the EFI entry. Thank you very much