If you charge a refundable security deposit and are connecting to Booking.com the security deposit needs to be manually added as a damage deposit in the Booking.com extranet.
The security deposit will be displayed to the guest at the time of booking however it is never a part of a total price as it is a refundable fee.

Therefore the total price showing to the guest on Booking.com would include accommodation + extra charges but the damage deposit amount would be displayed separately as in the screenshot below:

The booking in YesBookit includes the security deposit in the total, so the total amount will be higher.

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