A method and system for facilitating merchant-initiated online payments are disclosed. According to one aspect of the present invention, a payment service provider's server receives a user's request, via a merchant's server, to establish a merchant-initiated payment relationship or agreement. Accordingly, the payment service provider presents the user with options to customize the terms of the merchant-initiated payment agreement. After the agreement has been established and the terms customized, the merchant server communicates a merchant-initiated payment request to the pavement service provider for a transaction entered into with the user. The payment service provider's server processes the payment request after verifying that processing the payment does not exceed the user-customized terms of the agreement.