Payment Processing Fee Comparison

Payment processing fees are a fixed cost on every single order your ecommerce store processes, yet most brands never compare processors to find the best rate. On a $65 order, the difference between Shopify Payments at 2.9% + $0.30 and a negotiated Stripe rate at 2.5% + $0.30 is $0.26 per order. That sounds tiny until you multiply it by 2,000 monthly orders — the savings add up to $520 per month or $6,240 per year.

This calculator compares the five most common payment processors for ecommerce brands: Shopify Payments (Basic), Shopify Payments (Advanced/Plus), Stripe standard, PayPal standard, and a custom negotiated rate. For each processor, it shows the fee per order, total monthly cost, and the processing fees as a percentage of total revenue. The cheapest option depends on your AOV — lower AOVs are disproportionately affected by the fixed per-transaction fee ($0.30), while higher AOVs are more affected by the percentage rate.

For brands processing over $50K per month, negotiating a custom rate with Stripe or a payment processor is almost always worth the effort. Rates of 2.2% to 2.5% are achievable for established businesses with low chargeback rates. Shopify Plus merchants get access to better rates as well. The annual savings from a 0.3 to 0.5 percentage point reduction in processing fees can fund a significant portion of your CRO or retention program.

Processing fees are often the third or fourth largest variable cost per order after COGS, shipping, and ad spend. Include them in your contribution margin calculation and breakeven ROAS analysis for accurate profitability modeling.