WP Migrate DB Pro does support migrations to/from WordPress installations that have WordPress core installed in a subdirectory.
However, we do not support migrations between WordPress installations where WordPress core is installed in the default location for one website and installed in a subdirectory for the other website.
As such, the following is supported:
- Default installation → default installation
- Subdirectory installation → subdirectory installation
And the following is not supported:
- Default installation → subdirectory installation
- Subdirectory installation → default installation
Please also note that the name of the subdirectory used to install WordPress into should match on both websites, i.e. if using the directory “wp”, both WordPress installations should be using the directory name “wp”. Please don’t mix and match the directory names.