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Having your own merchant account does not necessarily mean it is cheaper at the end of the day. By the time you factor in customer service, chargeback fees, etc, the percentage is usually around the same as if you were a larger client with an IPSP.
However, having your own merchant account does offer you the ability to own your customers. For instance, if you want to leave your bank to go to a new one, you take your own data with you, something that does not happen with an IPSP, unless you specifically negotiated that into your contract, which is rare.
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