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Business merchant accounts are not free. There are various expenses related to the merchant account that will have to be paid. When you're choosing your bank merchant account consider all the fees, not just the transaction fees. Sometimes there is an application fee which is nonrefundable, regardless of whether the application is approved or rejected. Annual fees are charged once a year similar to what some consumer credit card companies charge individuals.
There can be a monthly account fee which will have to be paid even if there aren't any charges made during the month. If a charge is made there will be a transaction fee and a discount rate or percentage of the product's price. There can also be a minimum sales volume fee. If your account doesn't generate sales of specified minimum level you pay the volume fee. The fees are based on the risk the bank assumes by approving the account.
Online transactions are considered riskier than in person transactions because the physical card isn't swiped. It is easier for an online merchant to commit credit card fraud than a bricks and mortar business. Another factor considered in determining the fees is what type of business you conduct. Some types have a higher fraud incidence than others.