The YubiKey Manager can be used to check which applications are enabled on which interface and to enable or disable each application on each physical interface.
To find out which applications are enabled, select the Interfaces tab. A checkbox with a tick is shown next to each enabled applications. To change which applications are enabled, use the checkboxes to select the ones you want enabled and click Save Interfaces.
For the YubiKey 5Ci, any modifications made to the applications over the USB interface will also apply to the applications over Lightning®.
Once the desired applications have been selected, a lock code can be set to prevent changes to the set of enabled applications. This is done using the YubiKey Manager command line interface command
ykman config set-lock-code. The lock code is 16 bytes presented as 32 hex characters. For more information, see the YubiKey Manager (ykman) CLI & GUI Guide.