Getting paid online used to mean a merchant account, an underwriting call, and a developer. Today you can be accepting cards in an afternoon. The catch is that the easy setups and the flexible ones pull in opposite directions, and the fee structures are designed to be hard to compare. This guide walks through the handful of decisions that actually matter so you can start taking payments without boxing yourself in later.
Know the three ways to get paid online
A payment gateway on your own site
If you have your own website or app and want the checkout to live there, you want a gateway with a developer-friendly API and prebuilt checkout components. Stripe is the common default here because its documentation and hosted checkout let you go live quickly while still supporting custom flows as you grow. Braintree and Authorize.net are long-standing alternatives, and Adyen leans toward larger or international operations. This route gives you the most control and usually the cleanest customer experience, at the cost of a little setup work.
A hosted checkout or payment link
If you don't have a site to build on — or you just want to invoice someone and get paid — a payment link is the fastest path. You generate a URL or a button, the provider hosts the secure checkout page, and the money lands in your account. PayPal is the most recognized name for this and adds buyer trust for first-time customers, while Square offers clean invoices and links that share a login with its in-person tools. No code, no site, and almost no compliance burden on your end.
A store or platform with payments built in
If you're selling products, it's often easiest to let your storefront handle payments natively. Shopify Payments is built into Shopify so you're not wiring up a separate gateway, and most website builders offer a similar bundled option. You trade some flexibility for the convenience of one system that handles the cart, the checkout, and the payout together.
Understand what you'll actually pay
Most online providers advertise a flat rate in the neighborhood of a small percentage of each sale plus a fixed per-transaction fee. That flat pricing is genuinely simple and hard to beat when you're small. What the headline rate hides is everything around it: higher rates for manually keyed or international cards, currency conversion markups, chargeback fees, and monthly minimums on some plans. Read past the first number before you commit.
- Flat-rate pricing (a set percentage plus a few cents per transaction) is predictable and ideal for lower or uneven volume.
- Interchange-plus pricing exposes the underlying card-network cost and can be cheaper at higher volume — providers like Helcim and Stax lean this way.
- Watch for extras: chargeback fees, currency conversion, instant-payout fees, and per-refund handling that the headline rate leaves out.
- Check the payout schedule. Standard is usually a couple of business days; slow or held payouts can quietly strain cash flow.
Match the tool to how you sell
If you bill subscriptions or sell digital goods, look for a provider that handles recurring billing, dunning (retrying failed cards), and sales tax. Paddle and Lemon Squeezy act as merchant of record, meaning they take on collecting and remitting sales tax and VAT for you — a real time-saver for software and download businesses. For recurring bank debits rather than cards, GoCardless specializes in direct debit and tends to be cheaper for predictable invoices.
If some sales happen at a counter, a market stall, or a client's site, choose a provider that unifies online and in-person so you're not reconciling two systems. Square and SumUp pair online links or stores with card readers under one account and one dashboard, which keeps your reporting sane and your payouts in one place.
Recommended tools
- Stripe— Developer-friendly gateway for your own site or app.
- PayPal— Instant payment links and buyer trust with no site needed.
- Square— One account for online links and in-person card readers.
- Helcim— Interchange-plus pricing that pays off as volume grows.
- QuickBooks vs Xero— Decide where your payments should reconcile in your books.
- Browse all Payments & POS— Compare the full payments category.
Set it up without creating headaches later
- Verify your business details and bank account before your first sale — unverified accounts are the most common reason a first payout gets held.
- Connect your provider to your accounting tool so fees and payouts reconcile automatically; if you haven't settled that yet, the QuickBooks vs Xero comparison is a good starting point.
- Turn on fraud rules and a clear billing descriptor from day one — a single chargeback costs more than the fees you'd save by ignoring them.
- Test a real transaction end to end, including a refund, before you point customers at it.
The mistakes that actually hurt aren't about picking the wrong logo — they're held payouts from skipped verification, surprise fees on international or keyed-in cards, and building a heavily customized checkout before you've made a single sale. Start with the simplest setup that fits how you sell, confirm the money arrives, and add complexity only when volume justifies it. Moving up from a payment link to a full gateway later is easy; the reverse rarely is.
Not sure which pattern fits your business yet? Answer a few questions in build your stack and we'll suggest a payments setup — and the accounting and website tools around it — based on how you actually sell.
