The Hidden Cost of Square: Why B2B Invoice Payments Demand a Different Model

Square and Stripe have built powerful brands by making payments simple. For a coffee shop or a boutique retailer, their plug-and-play tools are a great fit. But mid-market companies processing millions in B2B invoice payments quickly discover the cracks: flat fees that balloon with volume, no access to interchange savings, and integrations that stop at the surface.

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For CFOs, these aren’t minor issues. They’re six-figure line items in the P&L.

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Flat Fees That Don’t Scale

Square charges 3.3% + $0.30 every time a customer pays an invoice with a card . Stripe comes in slightly lower at 2.9% + $0.30, plus another 0.4–0.5% if you use their invoicing tool .

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Those percentages sound small — until you do the math. A company processing $50M in card payments could be handing over $1–2.5M a year in fees . And here’s the kicker: with Square, you pay the same whether your customer uses a debit card, a premium rewards card, or a corporate purchasing card .

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That “simplicity” masks the fact that you’re subsidizing your customers’ rewards points out of your margin.

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The Level 3 Blind Spot

Corporate cards qualify for lower interchange rates if you pass along detailed invoice data (Level II and Level III). Done right, this can shave 0.5%–0.8% off every transaction — nearly a full percentage point .

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Stripe supports Level 2/3 data (if you build it into your workflow). Square doesn’t support it at all. That means a $10,000 invoice through Square costs you about $330, while a provider optimizing Level 3 could drop that closer to $200. Over a year, the delta is massive.

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Hidden Operational Costs

Beyond fees, there’s the back office. Square and Stripe aren’t designed to integrate cleanly with NetSuite, Sage Intacct, or Microsoft Dynamics. Finance teams end up manually reconciling payments, exporting CSVs, and patching together reports .

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That wasted time is a cost CFOs rarely see in the rate sheet — but it’s real. Case studies show mid-market firms reclaiming hundreds of hours a week just by moving off generic processors to B2B-focused platforms.

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A Smarter Path: Centime Merchant Services

Square and Stripe weren’t built for B2B invoice flows. Centime Merchant Services is.

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Interchange-Plus Pricing, Not Flat Fees: Instead of blending all card types into one high rate like Square, Centime uses an interchange-plus model so you capture the lowest possible cost on each transaction — especially critical for corporate cards.
Faster Access to Cash: Most credit card payments settle within one business day, and ACH within three. That means fewer delays and more predictability in your cash position.
Consolidated Deposits for Easier Reconciliation: No more chasing dozens of micro-deposits. Centime rolls everything into just two net deposits per day (one for cards, one for ACH), making reconciliation dramatically faster.
Transparent Fees, No Surprises: Fees are deducted right at settlement, so you see your true cost in real time — not buried in a confusing month-end statement.
Automated Chargeback Handling: With clearer visibility and more automation, disputes don’t drain staff time or delay collections.
ERP-Embedded, Not Bolted On: Payments feed directly into AP/AR and cash management, eliminating the manual reconciliation work that Square and Stripe leave behind.

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With Centime, merchant processing becomes a margin lever: lower effective rates, faster payouts, simpler books, and workflows built for the way mid-market finance teams actually operate.

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👉 Ready to see what you could save? Book a demo today.

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**Deposit placement through ICS is subject to the terms, conditions, and disclosures in the applicable agreements. Although deposits are placed in increments that do not exceed the FDIC standard maximum deposit insurance amount (“SMDIA”) at any one destination bank, a depositor’s balances at the institution that places deposits may exceed the SMDIA (e.g., before settlement for deposits or after settlement for withdrawals) or be uninsured (if the placing institution is not an insured bank). The depositor must make any necessary arrangements to protect such balances consistent with applicable law and must determine whether placement through ICS satisfies any restrictions on its deposits. A list identifying IntraFi network banks appears at https://www.intrafi.com/network-banks. The depositor may exclude banks from eligibility to receive its funds. IntraFi and ICS are registered service marks, and IntraFi Cash Service is a service mark, of IntraFi Network LLC.

^††3.0% Annual Percentage Yield (APY) as of 01/07/25. Deposit rate may adjust to current market rate and may change daily. Fees may reduce earnings.

*Centime is not a bank and is not authorized by any federal or state agency to engage directly in core banking activities.
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*All banking products and services available through Centime are provided by FNBO and are governed by the applicable agreements and related disclosures provided to you by FNBO. Member FDIC.
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‍*While Centime facilitates traditional banking activities (such as the acceptance of deposits or extensions of credit), these services are actually provided by our banking partner, FNBO.
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*Centime may provide support services to FNBO, as permitted by applicable law, to facilitate the delivery of its bank products and services.

**Deposit placement through ICS is subject to the terms, conditions, and disclosures in the applicable agreements. Although deposits are placed in increments that do not exceed the FDIC standard maximum deposit insurance amount (“SMDIA”) at any one destination bank, a depositor’s balances at the institution that places deposits may exceed the SMDIA (e.g., before settlement for deposits or after settlement for withdrawals) or be uninsured (if the placing institution is not an insured bank). The depositor must make any necessary arrangements to protect such balances consistent with applicable law and must determine whether placement through ICS satisfies any restrictions on its deposits. A list identifying IntraFi network bank

The Hidden Cost of Square: Why B2B Invoice Payments Demand a Different Model

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