About 12; min
Every online sale loses 2.9-3.5% to payment processing. On $100,000 in annual revenue, that’s $2,900-3,500 you never see. The processor you choose decides how much you keep. We compared 6 payment processors on the fees that actually hit your bank account — not just the advertised rates, but chargebacks, currency conversion, and the hidden costs buried in the fine print.
All fees verified March 2026 from official websites.
Best Payment Processors, Ranked
| # | Processor | Online rate | In-person rate | Best for |
|---|---|---|---|---|
| 1 | Stripe | 2.9% + 30¢ | 2.7% + 5¢ | Online businesses, SaaS, marketplaces |
| 2 | Square | 2.9% + 30¢ | 2.6% + 15¢ | Retail, restaurants, in-person |
| 3 | PayPal | 3.49% + 49¢ | 2.29% + 9¢ | Customer trust, quick setup |
| 4 | Shopify Payments | 2.9% + 30¢ | 2.7% + 0¢ | Shopify store owners |
| 5 | Adyen | IC++ (~2.3-2.5%) | IC++ variable | Enterprise, high-volume |
| 6 | Helcim | IC++ (~2.4% avg) | IC++ (~1.9% avg) | Cheapest for mid-volume |
1. Stripe — Best for Online Businesses
Rates: 2.9% + 30¢ online, 2.7% + 5¢ in-person, +1.5% international, +1% currency conversion.
Stripe is the default for online businesses. Developer-friendly API, 135+ currencies, subscription billing, marketplace payouts (Stripe Connect), and fraud prevention (Radar). If you sell online and need flexibility, Stripe handles every payment scenario.
Why #1: Most integrations, best documentation, handles every business model from one-time sales to usage-based billing. The 2.9% + 30¢ rate is industry standard — you won’t find significantly lower without going interchange-plus.
The catch: 2.9% is flat-rate, not interchange-plus. High-volume merchants (>$80K/month) save money on interchange-plus pricing from Helcim or Adyen.
2. Square — Best for In-Person Sales
Rates: 2.6% + 15¢ in-person, 2.9% + 30¢ online, 3.5% + 15¢ manually keyed.
Free card reader, free POS app, free online store. Square’s ecosystem handles everything a physical business needs — payments, inventory, employees, loyalty, banking. One app, one login.
Why it ranks high: $0 chargeback fees. First card reader free. Full business operating system included. For brick-and-mortar businesses, Square replaces 3-4 separate tools.
3. PayPal — Most Recognized Brand
Rates: 3.49% + 49¢ online (PayPal Checkout), 2.29% + 9¢ in-person (Zettle).
The most expensive online rate on this list. But PayPal’s blue button converts hesitant buyers. Customer trust is PayPal’s product — people buy from unfamiliar stores when PayPal is an option.
Best strategy: Use Stripe as primary processor, add PayPal as a checkout option. Capture the 10-15% of customers who only trust PayPal without paying PayPal’s rate on every transaction.
4. Shopify Payments — Best for Shopify Stores
Rates: 2.9% + 30¢ (Basic), 2.6% + 30¢ (Shopify), 2.4% + 30¢ (Advanced). 0% third-party transaction fees.
If you run a Shopify store, use Shopify Payments. Any other gateway adds a 2% surcharge on top of the gateway’s own fees. Shopify Payments eliminates that surcharge. Powered by Stripe on the backend.
5. Adyen — Best for Enterprise
Rates: Interchange++ pricing. Adyen’s markup: ~0.6% + 13¢. Total effective rate: ~2.3-2.5% for most transactions.
Adyen processes payments for Nike, Uber, Spotify, and Microsoft. Interchange-plus pricing means you pay the actual card network fee + a small Adyen markup. Cheaper than flat-rate for high-volume merchants. But: minimum invoice requirements and enterprise-focused onboarding make it impractical for small businesses.
6. Helcim — Cheapest for Growing Businesses
Rates: Interchange++ with no monthly fee. Average effective rate: ~2.4% online, ~1.9% in-person.
Helcim is the only interchange-plus processor with no monthly fee, no contract, and transparent pricing. For businesses processing $10,000-100,000/month, Helcim is typically the cheapest option. The catch: smaller integration ecosystem than Stripe or Square.
Fee Comparison: $10,000/Month in Sales
| Processor | Monthly fees (200 online transactions) | Annual cost |
|---|---|---|
| Helcim | ~$260 | $3,120 |
| Adyen | ~$270 | $3,240 |
| Stripe | $350 | $4,200 |
| Square | $350 | $4,200 |
| Shopify Payments | $350 | $4,200 |
| PayPal | $447 | $5,364 |
Helcim saves $1,080/year over Stripe at $10K/month revenue. PayPal costs $2,244/year more than Helcim. The gap widens with volume.
Hidden Fees to Watch
| Fee | Stripe | Square | PayPal |
|---|---|---|---|
| Chargebacks | $15 | $0 | $20 |
| International | +1.5% | Same rate | +1.5% |
| Currency conversion | +1% | N/A | +3-4% |
| Refund fee kept | $0 | $0 | $0.49 |
| Instant payout | 1% | 1.75% | 1.75% |
Who Should Pick What
Online business (SaaS, e-commerce, digital): Stripe. Best API, most integrations, 135+ currencies. The default for a reason.
Physical store or restaurant: Square. Free POS, free reader, full business ecosystem. Best in-person experience.
Shopify store: Shopify Payments. Avoid the 2% third-party gateway surcharge. No other option makes financial sense.
Processing $10K+/month, want lowest rates: Helcim. Interchange-plus pricing with no monthly fee saves $1,000+/year over flat-rate processors.
Enterprise ($1M+/month): Adyen. Lowest rates at scale, 150+ payment methods, global coverage.
Need maximum checkout conversion: Stripe (primary) + PayPal (secondary). Capture every buyer preference without paying PayPal’s rate on every sale.
Frequently Asked Questions
Which payment processor has the lowest fees?
Helcim (interchange-plus, ~2.4% average online). For flat-rate, Stripe and Square tie at 2.9% + 30¢. PayPal is the most expensive at 3.49% + 49¢.
Can I switch processors later?
Yes, but customer saved payment methods don’t transfer. Subscription customers need to re-enter cards. Plan 1-2 weeks of disruption. Pick right the first time.
Do I need a merchant account?
Not with Stripe, Square, or PayPal — they act as the merchant of record. Adyen and traditional processors require a merchant account. For most small businesses, Stripe or Square is simpler.
All fees verified March 2026. Rates may vary by business type and volume.
