When you issue a refund, your customer gets back what she paid, plus sales tax, and your business is reimbursed a portion of the fees paid to your Merchant Account Provider. It’s standard procedure for your provider to only reimburse Interchange and not its markup. However, if you’re on a Tiered or Flat rate plan, you will not receive any processing fees back.
It is also typical for your provider to charge an authorization fee when processing refunds. This is a small fee applied to each transaction that shouldn't cost you more than a few cents. However, merchant statements are complex, making it easy for providers to hide additional fees on refunds.
For more on how processing refunds click here