Comparing Gateway Fee Structures for B2B SaaS

Inconsistent fee structures make cost comparisons tricky

Choosing a payment gateway is rarely straightforward. Gateway providers use different billing models that often lack transparency. The result is a confusing web of fixed fees, percentage rates, minimums, and transaction-specific surcharges.

For accounting teams in SaaS companies, this creates a major challenge when trying to evaluate true costs across providers. You may find a provider advertising 2.9% + 30¢ per transaction, but that only covers a basic domestic card transaction. As soon as you accept international cards, high-risk transactions, or platform payouts, the costs often rise.

Additional variables like cross-border fees, refund costs, chargeback penalties, currency conversion margins, and batch processing charges vary widely. Comparing Authorize.net vs Stripe, for example, shows not only different base rates but differences in reporting, support, and included services.

This complexity makes apples-to-apples cost evaluation nearly impossible without deeper analysis.

Fee visibility enables better financial planning

Accounting teams benefit most when they understand all cost layers of their payment stack. That starts by requesting a full fee schedule from your provider—not just the base rate.

With visibility into all applicable charges, finance teams can model transaction costs by type, geography, volume, and customer behavior. This allows for more accurate forecasting of gross revenue, net revenue, and fees.

Gaining transparency also enables your team to identify trends over time. For example, if a growing percentage of your customers are based outside the US, cross-border and FX-related costs may become a larger share of your total fees.

That level of clarity supports better vendor decisions and gives leverage during rate negotiations.

Avoid picking gateways by headline rates

Low advertised rates can be misleading. They may only apply under limited conditions and often exclude fees that will affect your actual cost per transaction.

For instance, Stripe’s 2.9% + 30¢ rate doesn’t include international cards or currency conversion. Authorize.net may offer lower per-transaction costs but adds monthly fees and separate gateway and processor charges.

Basing decisions on headline rates alone can lead to higher actual costs after accounting for refund policies, chargebacks, support levels, and how quickly funds are deposited.

Instead of focusing only on one rate, evaluate each provider based on the overall fee structure, support responsiveness, integration reliability, and reporting quality. These factors all affect the total cost of ownership.

Normalize and monitor gateway fee data at scale

As SaaS businesses grow, so does the volume and complexity of transactions. Tracking payment gateway fees manually quickly becomes unsustainable.

Use billing or accounting platforms that allow you to normalize fee structures across providers. This helps maintain a consistent view of gateway performance, effective rates, and trends over time.

Modern platforms make it easier to connect raw transaction data with associated fee details. This gives accounting teams accurate reporting on gross vs net revenue and flags unexpected spikes in transaction costs.

When you evaluate multiple providers—such as comparing Authorize.net vs Stripe—structured reporting helps you assess true ROI. This becomes especially important during gateway migrations or when expanding into new markets.

Payment gateway decisions are rarely permanent. A structured and scalable way to compare gateway fee data enables your business to adapt as your pricing, customers, and revenue models evolve.