For the majority of the accommodations available, Booking.com works with an agency model. That means that payments are collected directly by the properties.
Most of the accommodations accept and require a credit card. Some accommodations do not accept credit cards - prepayment for rooms at these properties should be made by bank transfer. Additionally, more than 300,000 accommodations can be prepaid via Paypal, iDeal, Sofort and Debit card.
You can check which payment method is accepted by the particular accommodation on the property's description page, or make easily filter by payment method.