Migrate different WP directories under same domain

Currently, I have an existing website (www.example.com). For this domain, I have 2 sub-directories with 2 different WP installations.

https://www.example.com/ ----> Main site with WP
https://www.example.com/blog/ —> A sub-directory with dedicated WP install
https://www.example.com/store/ —> Another sub-directory with dedicated WP install

If I use the Cloudways Migrator plugin, I can only successfully migrate the main (https://www.example.com/).

Do I need to do the same process again with the other WP installs? Which means I will have to migrate the site 3 times? Or is there a better way to do this?

You´ll have to do the migration 3 times.