A merchant account is another important term when talking about electronic payment services. When an online transaction is successfully completed, the funds are transferred from the purchaser's account to your merchant account. A merchant account is a special kind of bank account that exclusively holds the funds from credit and debit card transactions. To accept online payments, you need to set up a merchant account with your payment provider. Funds accumulating in your merchant account are transferred to your organization's bank account on a regular basis.