Most merchants focus on the processing rate when they evaluate their merchant account. That makes sense — it's the biggest number and the one most visible in a sales conversation. But there's a second layer of fees that never comes up in the sales pitch and rarely gets explained on the statement. These fees don't have anything to do with processing transactions. They just compound quietly, month after month, and most merchants pay them without knowing what they're for.
Here are five of the most common ones, what they actually are, and which ones you can do something about.
1. The PCI Non-Compliance Fee
PCI DSS — the Payment Card Industry Data Security Standard — requires businesses that accept card payments to complete an annual self-assessment questionnaire and meet certain security standards. If you haven't done it, many processors charge a monthly non-compliance fee until you do.
The fee varies by processor, but it shows up on statements labeled as "PCI non-compliance," "security non-compliance," or sometimes more vaguely as a "regulatory fee." It's charged every month you remain out of compliance, and it can run for years without the merchant realizing what it is or how to fix it.
The PCI self-assessment questionnaire is a form — not a technical audit. Most small businesses can complete it in under an hour through their processor's compliance portal. If you're paying a non-compliance fee, completing the SAQ makes it stop immediately. This is entirely avoidable.
Note: some processors charge a separate PCI compliance fee for being compliant. That's different from a non-compliance penalty, and it's worth asking about when you're evaluating a new processor — you shouldn't be paying for both.
2. The Monthly Minimum Fee
Some processing agreements include a monthly minimum — a floor on the processing fees you generate in a given month. If your actual fee volume falls below that minimum, the processor charges you the difference.
Here's how it works: if your agreement has a $25 monthly minimum and you only generated $12 in processing fees for the month, you pay an additional $13. If you had a slow month and generated no fees at all, you pay the full minimum.
This hits hardest on seasonal businesses — slow months generate low volume, which means low processing fees, which means the monthly minimum kicks in on top of everything else. It's also rarely mentioned in the sales conversation, and merchants often don't notice it for months because it shows up as a separate small line item.
What to do: Check your agreement for any mention of "monthly minimum," "minimum monthly fee," or "minimum discount." If it's there and you're regularly processing enough volume to exceed it, you may never see it — but if you have slow seasons, it's worth knowing about before it shows up on a statement.
3. The Batch / Settlement Fee
Every time you close your batch — usually at the end of each business day — and send your transactions to the processor for settlement, many processors charge a small per-batch fee. It's typically a flat amount regardless of how many transactions are in the batch.
The fee itself is small. But if you're closing a batch every business day, you're paying it 250+ times per year. Those small amounts add up to a meaningful annual cost that's never mentioned when the account is being pitched to you.
What to do: Look for "batch fee," "settlement fee," or "close batch fee" on your statement. If it's there, ask whether it's negotiable. Some processors will waive or reduce it for established accounts; others won't, and knowing the cost is still worth something when you're comparing options.
4. The Statement Fee
A monthly charge, usually in the $5–$15 range, just for receiving your statement — whether electronically or on paper. It has nothing to do with processing transactions. It's a pure administrative fee charged for the act of producing your bill.
This one appears under a variety of labels: "statement fee," "reporting fee," "account access fee," "e-statement fee." Some processors charge it for paper statements only and waive it if you opt into electronic delivery. Others charge it regardless.
It's a small number on any given month. Over a year, it's $60–$180 you're paying for the privilege of seeing what you owe. It's worth knowing it's there.
What to do: Ask your processor directly whether the statement fee is waiveable. It's one of the more negotiable line items, particularly if you have significant monthly volume or a long relationship with the processor. Some will waive it without much pushback; others won't.
5. The Annual Fee
Many processors charge an annual fee — sometimes called an "annual account fee," "annual maintenance fee," or "membership fee." It typically appears once per year, either in December or on the anniversary of your account opening. It can range from a nominal amount to something more significant, depending on the processor.
Because it shows up infrequently, it tends to get lost. Merchants either don't notice it or assume it's a legitimate cost of processing without questioning it. It's also rarely mentioned when you're signing up, because the person selling you the account is focused on the processing rate, not a fee that shows up once a year.
What to do: Ask your processor directly, in writing: "Do you charge an annual fee?" before signing anything. If you already have an account, look at your December statements or your account anniversary month and see if there's an unfamiliar charge. If you find one and weren't told about it, that's worth a conversation.
The Bigger Picture
None of these fees are enormous on their own. That's the point. They're sized to be easy to overlook — small enough that most merchants don't make a call about them, large enough to be worth charging. Added together, and applied month after month and year after year, they can represent hundreds of dollars in annual cost that you never agreed to knowingly.
The free audit covers all of this. We go line by line through your statement, identify every fee by name and type, and flag anything you're paying that is negotiable, avoidable, or unexplained. Most merchants who go through the process are surprised by something.