I'm going to post all the commands I use because I think that may be easier to follow. All the commands I'm posting will include the --dry-run option so if anyone tries to copy/paste this into their terminal, no actions will be taken. Instead it will show you what is going to happen if you ran the command without any changes.

As I mentioned before, each partition will require it's own command. The easiest way is using lsblk. Below is my current setup and here you can see I have 5 partitions. One partition is a swap so I will only be working with 4 partitions, /, /boot, /boot/efi and /home:

dell:~ $ lsblk
NAME                  MAJ:MIN RM   SIZE RO TYPE  MOUNTPOINTS
nvme0n1               259:0    0 953.9G  0 disk  
├─nvme0n1p1           259:1    0   500M  0 part  /boot/efi
├─nvme0n1p2           259:2    0  62.5G  0 part  
│ └─luks1-dell        253:0    0  62.5G  0 crypt 
│   ├─vg_dell-lv_boot 253:1    0   500M  0 lvm   /boot
│   ├─vg_dell-lv_swap 253:2    0     8G  0 lvm   [SWAP]
│   ├─vg_dell-lv_root 253:3    0    38G  0 lvm   /
│   └─vg_dell-lv_home 253:4    0    16G  0 lvm   /home
├─nvme0n1p3           259:3    0   600G  0 part  
├─nvme0n1p4           259:4    0 270.9G  0 part  
└─nvme0n1p5           259:5    0    20G  0 part 

It's good to first check what partitions you are using. My Raspberry Pi's (ARM) only have / and /boot for example.

The following rsync commands are what I use to make a complete backup of my system. I do exclude a number of directories because they are for temporary stuff like ram, processes or even devices/drives. It's also important to exclude the specified backup directory to avoid recursing into the backup directory and filling up your storage space.

I have a manual backup location and automated backup location. The following is for my manual backup location in /backup/main on my system. This location can be changed to wherever you want your backup.

# Backup
# /
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=/backup/* --exclude=/boot/* --exclude=home/* --exclude=proc/* --exclude=sys/* --exclude=dev/* --exclude=tmp/* --exclude=run/* --exclude=mnt/* --exclude=media/* '/' '/backup/main/'

# /boot/
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found '/boot/' '/backup/main/boot/'

# /boot/efi/
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found '/boot/efi/' '/backup/main/boot/efi/'

# /home/
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found --exclude=.cache/* '/home/' '/backup/main/home/'

# Restore
# /
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=/backup/* --exclude=/boot/* --exclude=home/* --exclude=proc/* --exclude=sys/* --exclude=dev/* --exclude=tmp/* --exclude=run/* --exclude=mnt/* --exclude=media/* '/backup/main/' '/'

# /boot/
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found '/backup/main/boot/' '/boot/'

#/boot/efi/
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found '/backup/main/boot/efi/' '/boot/efi/'

# /home
rsync --dry-run --archive --acls --one-file-system --xattrs --hard-links --sparse --verbose --human-readable --partial --progress --numeric-ids --delete --exclude=lost+found --exclude=.cache/* '/backup/main/home/' '/home/'

It's been a while since I last researched these options so I'll give a brief explanation of the types of options I used. I'd suggest having a look online or at the man page to get a better idea of what each option does.

Options:

--dry-run Only displays what rsync will do, remove this once you are ready to commit any syncs/changes

archive --acls --one-file-system --xattrs --hard-links --sparse Helps preserve file attributes and other information. I think hard-links is also used to reduce backup size. There are many rsync guides that will give a better explanation of how hard-links work

verbose --human-readable --partial --progress will display visual data about what rsync will do

--numeric-ids I use this because I store multiple device backups on a single drive which gets copied to other storage devices. This stores file ownership information as numeric values to prevent ownership issues when restoring

--delete this will force the destination directory to match the source directory completely. If you delete a file from the source directory, when you perform a sync, it will delete the same fie in the destination directory. This can be dangerous if you are not prepared for it. This is why --dry-run is so important and useful.

Extra options: My automated scripts use 2 additional options. I keep a rolling set of 4 backups (One month of weekly backups). I create a new directory /backup/updating and use a symlink from/backup/latest that points to the most recent automated backup. After the backup is created, I rename /backup/updating to something with a timestamp like /backup/backup_2026-07-01_1782882013

--mkpath will create any non existing directories specified in the command

--link-dest=/backup/latest/ will use the unchanged files from this directory to help reduce backup sizes. I think this is called an incremental backup

This has been the most reliable way to handle backups for myself. I do run into issues with docker/podman containers sometimes and will have to manually delete those directories. I haven't figured out how to deal with that issue yet but fortunately it's easy to find those directories. Running the command will give errors about what directories can't be removed which makes it easy to hand delete them in another terminal window.