What you need to set up payments on your website
To accept payments on your website, you need three things: a payment processor (the company that handles the transaction), a merchant account (the bank account where money lands), and integration code (the software that connects your site to the processor). Most modern processors bundle the merchant account into their service, so you do not need to set them up separately anymore.
The processor is the middleman. When a customer enters their card details on your site, the processor verifies the card with the bank, holds the money temporarily, and then deposits it into your account—usually within one to three business days. The processor charges you a fee for this work, typically 2.2% to 3.5% of each transaction plus a flat per-transaction fee of $0.25 to $0.50.
You do not need to be a large company to start. Processors like Stripe, Square, PayPal, and Shopify Payments will work with sole proprietors and small businesses. The main difference between processors is how they charge, what payment methods they support, and how easy they are to integrate into your specific website platform.
Key Takeaways
- A payment processor handles the transaction, a merchant account receives the money, and integration code connects them to your website—most modern processors combine all three.
- Stripe, Square, PayPal, and Shopify Payments are the most common choices for small websites, each with different fee structures and ease of setup.
- You will need to provide business information, a bank account for deposits, and proof of identity during the signup process.
- Integration takes anywhere from one hour (using a pre-built plugin) to several days (custom code), depending on your website platform and the processor you choose.
- Processors hold funds for fraud review or chargeback disputes, which can delay deposits by a few days to several weeks in some cases.
Choosing between the major payment processors
The four most widely used processors for small websites are Stripe, Square, PayPal, and Shopify Payments. Each one works differently depending on whether you have a custom-built site, a WordPress site, a Shopify store, or a simple landing page.
Stripe is the most flexible. It works with almost any website platform and requires some technical setup—you or a developer will need to add code to your site. Stripe charges 2.9% plus $0.30 per transaction for card payments. It supports credit cards, digital wallets (Apple Pay, Google Pay), and bank transfers. Stripe is best if you have a developer on hand or are comfortable with technical documentation.
Square is simpler to set up without code. You can create a payment link, embed a button on your site, or use Square's online store builder. Square charges 2.9% plus $0.30 per card transaction. It also offers Square Online, a full website builder with payments built in. Square is best if you want minimal technical work and do not mind their website builder limitations.
PayPal has been around the longest and many customers trust it. You can add a PayPal button to your site without code, or integrate it more deeply if you have a developer. PayPal charges 3.49% plus $0.49 per transaction for standard payments, which is higher than Stripe or Square. PayPal is best if your customers already have PayPal accounts or if you are selling internationally.
Shopify Payments only works if you use Shopify as your website platform. It charges 2.9% plus $0.30 per transaction and is built directly into Shopify's dashboard. Shopify Payments is best if you are already using Shopify or planning to move to it.
What information you will need to provide
Every processor requires you to verify your identity and business before you can accept payments. The signup process typically takes 10 to 20 minutes, but approval can take anywhere from a few minutes to several business days depending on the processor and your situation.
You will need to provide: your legal name and address, your Social Security Number or Tax ID, your business name and type (sole proprietor, LLC, corporation), your website URL, and a bank account where deposits will land. The bank account must be in your name or your business name—you cannot use someone else's account.
Some processors also ask for a photo ID, a brief description of what you sell, and your expected monthly transaction volume. If you have been in business for less than a year or have a thin credit history, the processor may ask for additional documentation or place a hold on your first few deposits while they monitor your account for fraud.
How to integrate payments into your website
Integration means connecting your website to the payment processor so that when a customer clicks "Pay," the processor handles the transaction. The method depends on what platform your website runs on.
If you use WordPress, install a plugin like WooCommerce, Easy Digital Downloads, or Gravity Forms. Each plugin has built-in connectors for Stripe, PayPal, and Square. You paste your processor's API keys into the plugin settings, and the plugin handles the rest. This takes 30 minutes to an hour if you follow the processor's documentation.
If you use Shopify, payments are already built in. Go to Settings > Payments and choose Shopify Payments or add Stripe, PayPal, or Square as an alternative. No code required—just connect your bank account and you are done.
If you have a custom-built website or use a platform like Webflow, you will need a developer to add the processor's code. Stripe and Square both provide code libraries (SDKs) and detailed documentation. A developer familiar with your site's language (JavaScript, Python, PHP, etc.) can usually integrate a basic payment form in a few hours. More complex setups—like subscription billing or split payments—take longer.
If you want no code at all, use Square's payment links or PayPal's button tool. You create a link or button in the processor's dashboard, copy the code, and paste it into your website's HTML. Customers click the link or button and are taken to a payment page hosted by the processor. This works but gives you less control over the look and feel of the checkout experience.
Fees, deposits, and what happens to your money
Payment processors charge in three ways: a percentage of the transaction (interchange fee), a flat per-transaction fee, and sometimes a monthly fee for advanced features. For most small websites, you only pay the percentage and per-transaction fee—there is no monthly charge unless you add extra services.
Here is what a typical transaction costs: A customer pays $100. Stripe charges 2.9% ($2.90) plus $0.30, for a total of $3.20. You receive $96.80. The processor keeps the $3.20. This happens for every transaction.
Money does not land in your bank account immediately. Most processors deposit funds once per day, usually between 24 and 72 hours after the transaction. Some processors hold funds longer if they suspect fraud or if a customer disputes the charge. During a chargeback dispute—when a customer tells their bank the charge was unauthorized—the processor can hold the money for 30 to 90 days while the dispute is investigated.
Processors also charge chargeback fees if a customer disputes a transaction. These fees range from $15 to $100 per dispute, on top of the money they refund to the customer. If you have too many chargebacks (usually more than 1% of your transactions), the processor can suspend your account or raise your fees.
Security and fraud protection
You do not store customer card details on your own website. When a customer enters their card number, the payment processor receives it directly—your website never sees it. This is called PCI compliance, and it is a legal requirement. If you try to store card details yourself, you become liable for breaches and face heavy fines.
All major processors use encryption and fraud detection to protect transactions. They monitor for patterns like multiple failed attempts, cards from different countries, or unusually large orders. If the processor suspects fraud, it can decline the transaction or flag it for manual review.
You can add extra fraud protection by requiring 3D Secure authentication (a second password the customer enters), checking the card's billing address against the shipping address, or using a service like Stripe Radar that scores each transaction for fraud risk. These tools reduce chargebacks but can also decline legitimate transactions, so use them carefully.
Troubleshooting common integration problems
The most common issue is API keys not working. Every processor gives you two keys: a public key (safe to show on your website) and a secret key (keep this private). If you paste the wrong key or paste the secret key in the wrong place, transactions will fail. Check the processor's documentation to confirm which key goes where.
Another frequent problem is test mode vs. live mode. When you first integrate, the processor gives you test keys that let you make fake transactions without charging anyone. You must switch to live keys before real customers can pay. Forgetting this step means your site looks like it works, but no money actually changes hands.
HTTPS is required. If your website does not use HTTPS (you will see a lock icon in the browser address bar), most processors will not let you accept payments. You need an SSL certificate, which most web hosts provide free or for a small annual fee. If you do not have HTTPS, your processor will reject the connection.
If customers see an error message during checkout, check your processor's dashboard for logs. Most processors show you exactly what went wrong—a declined card, a mismatched address, a timeout, or a configuration error. The error message usually tells you what to fix.
Frequently Asked Questions
How long does it take to start accepting payments after I sign up?
Processor approval usually takes a few minutes to a few business days. Once approved, integration takes 30 minutes to a few hours if you use a plugin or pre-built solution, or a few days if you need custom code. You can be live within 24 hours in most cases, assuming your website is already built.
Can I use multiple payment processors on the same website?
Yes. Many websites offer Stripe, PayPal, and Apple Pay side by side so customers can choose. This increases your transaction success rate because if one processor declines a card, the customer can try another. The downside is managing multiple accounts and fee structures. Most small websites stick with one or two processors.
What happens if a customer disputes a charge?
The processor notifies you and holds the money while investigating. You have a chance to provide evidence (an order confirmation, shipping proof, or customer communication) that the charge was legitimate. If the processor sides with you, you keep the money. If they side with the customer, the money is refunded and you pay a chargeback fee. The whole process takes 30 to 90 days.
Do I need a business license to accept payments online?
Requirements vary by location and what you sell. Most processors do not ask for a license during signup, but your local government may require one. Check with your city or county before you launch. Some processors will ask for a license if they flag your account for review.
Can I accept payments without a website?
Yes. Square and PayPal both let you create a payment link that you can send via email or text message. Customers click the link and pay without visiting your website. This works for invoices, donations, or one-off sales, but it is not ideal for a storefront.