Stop the virtual machine and execute the following steps on the host.
In case its not installed yet, you need the following tools
sudo dnf install libguestfs-tools-c
Locate the image files on your host. On Fedora that is
cd ~/.local/share/gnome-boxes/images
Identify the root partition of your image that you want to increase
virt-filesystems --long --parts --blkdevs -h -a <my-current-fedora-image>
Name Type MBR Size Parent
/dev/sda1 partition 83 1,0G /dev/sda
/dev/sda2 partition 8e 19G /dev/sda
/dev/sda device - 20G -
In my example that is /dev/sda2 = <identified-partition>
Create an empty image file in the correct format with the new root partition file size
qemu-img create -f qcow2 -o preallocation=metadata <my-new-fedora-image> <the-file-size-in-GB>G
Resize the root partition of the current image to the new image
virt-resize --expand <identified-partition> <my-current-fedora-image> <my-new-fedora-image>
Rename the new image file name to the old one so that GNOME Boxes will use it instead of the old one but keep the other one around as backup
mv <my-current-fedora-image> <my-old-fedora-image>
mv <my-new-fedora-image> <my-current-fedora-image>
This is all you have to do on the host. Now start the virtual machine with the increased root disk size, log in, and execute the following steps on the virtual machine.
Resize the partition that you identified for copying
sudo pvresize <identified-partition>
Identify the root filesystem name to extend
df -h
In my example that is /dev/mapper/fedora-root = <identified-filesystem>
Extend its logical volume size to make the additional space usable
sudo lvextend -r -l +100%FREE <identified-filesystem>
Source: https://www.reddit.com/r/gnome/comments/3ijfm5/cant_increase_vm_disk_size_in_gnome_boxes/