Currently, the InnoDB system tablespace can only be automatically encrypted/decrypted by the background encryption threads if innodb_encrypt_tables=ON|FORCE, innodb_encryption_threads>0, and innodb_encryption_rotate_key_age>0. There is no way to manually encrypt/decrypt the tablespace.

File-per-table tablespaces can be manually encrypted with:

ALTER TABLE tab ENCRYPTION=YES;

File-per-table tablespaces can be manually decrypted with:

ALTER TABLE tab ENCRYPTION=NO;

Some users want a similar method that would allow them to manually encrypt/decrypt the InnoDB system tablespace.

This is loosely related to MDEV-14571, since both issues are related to the fact that the system tablespace can only be encrypted/decrypted by the background threads.