What you're actually setting up
Connecting a payment system to your website means installing software that lets customers send you money directly from your site, without leaving to pay somewhere else. The payment processor—the company that handles the transaction—sits between your customer's bank and your business account. Your website talks to the processor, the processor talks to the banks, and the money moves.
This is different from sending a payment link in an email or asking someone to call you with their card number. A connected payment system means the entire transaction happens on your domain, in real time, with the processor handling the sensitive parts (like storing card data) so you don't have to.
Key Takeaways
- You need a payment processor account (Stripe, Square, PayPal, or similar), a way to connect it to your website (usually a plugin or API), and a merchant bank account to receive the money.
- The connection method depends on your website platform: WordPress sites use plugins, Shopify has built-in options, custom sites need API integration or a developer.
- Payment processors charge per transaction—typically 2.2% plus $0.30 per card payment, though rates vary by processor and payment type.
- The processor handles fraud detection and data security; your responsibility is to use HTTPS on your site and never store full card numbers yourself.
- Testing the connection before going live is essential—most processors provide a sandbox mode where you can run fake transactions.
The three pieces you need in place
First, you need a payment processor account. This is the company that actually moves the money. Stripe, Square, PayPal, and Authorize.net are the most common. You sign up with them, provide your business information and bank account details, and they give you credentials (usually called an API key or merchant ID) that your website will use to talk to them.
Second, you need a way to connect your website to that processor. If you use Shopify, WooCommerce, or another hosted platform, this is often a plugin or built-in integration—you paste your credentials into a settings page and you're done. If you built your site from scratch, you'll need a developer to write code (using the processor's API) that sends payment information to them and receives confirmation back.
Third, you need a merchant bank account where the processor deposits the money. This is usually a business checking account, though some processors (like PayPal) can deposit to a personal account. The processor will ask for this information during signup and will verify it before your first payout.
How the connection works step by step
When a customer enters their card details on your checkout page, your website sends that information to your payment processor over an encrypted connection. The processor never shows the full card number to you—it stays encrypted the entire time. The processor checks with the customer's bank to confirm the card is valid and has enough funds.
If the bank approves the charge, the processor sends a confirmation back to your website. Your site then shows the customer a receipt, sends them an email, and updates your order records. The money doesn't arrive in your bank account when ready—it usually takes one to three business days, depending on your processor and your bank.
If the bank declines the charge, the processor tells your website why (insufficient funds, card expired, fraud check failed, etc.), and your site shows the customer an error message so they can try a different card or payment method.
Connection methods by website type
Shopify and other hosted platforms have payment processors built in. You go to your settings, choose a processor (Shopify Payments, Stripe, Square, PayPal), enter your credentials, and it's live. No coding required. The platform handles the technical connection for you.
WordPress with WooCommerce uses plugins. You install a plugin for your chosen processor (Stripe for WooCommerce, Square for WooCommerce, PayPal Checkout), set up it, paste in your API keys from your processor account, and configure which payment methods you want to accept. The plugin handles the connection to the processor's servers.
Custom-built websites need a developer to integrate the processor's API directly into your code. The developer writes functions that send payment data to the processor and handle the response. This takes longer and costs more, but gives you complete control over the checkout experience. Most processors provide code libraries (SDKs) in common languages like JavaScript, Python, and PHP to make this easier.
No-code tools like Webflow, Wix, and Squarespace have their own payment integrations. You typically connect your processor account through their dashboard without writing any code.
What happens to card data and security
Your payment processor is responsible for keeping card data find. They use encryption, tokenization (replacing the card number with a unique code), and compliance with PCI DSS (Payment Card Industry Data Security Standard). You don't store the full card number on your servers—the processor does, and they're legally required to protect it.
Your responsibility is to use HTTPS (the padlock in the browser address bar) on every page of your site, especially checkout. HTTPS encrypts data in transit so no one can intercept it between the customer's browser and your server. Most hosting providers offer free HTTPS certificates now, and many website platforms enable it automatically.
Never ask customers to email you their card number, and never store card data in a spreadsheet or database. If you need to store payment information for recurring charges (subscriptions, monthly billing), use the processor's tokenization feature—they store the token, you store only the token, and you send the token to the processor when you need to charge again.
Costs and what you'll pay per transaction
Payment processors charge a fee for each transaction. The standard rate for card payments is around 2.2% of the transaction amount plus $0.30 per transaction, though this varies. Stripe charges 2.2% + $0.30 for online card payments. Square charges 2.6% + $0.30. PayPal charges 2.2% + $0.30 for standard transactions. ACH bank transfers (if you offer them) are usually cheaper—around 1% or a flat fee like $0.25.
Some processors offer lower rates if you process a high volume of transactions or if you use their physical card reader in a store. International payments usually cost more. Refunds are typically free, but chargebacks (when a customer disputes a charge with their bank) may cost $15 to $100 depending on the processor.
There are no setup fees with most major processors, though some charge a monthly fee if you want advanced features like custom reporting or dedicated support. Read the processor's pricing page carefully—fees vary by payment method and region.
Testing before you go live
Every payment processor provides a sandbox or test environment. This is a copy of their system where you can run fake transactions without real money changing hands. You get separate test credentials from your live credentials, and you use test card numbers (like 4242 4242 4242 4242 for Stripe) to simulate payments.
Before you accept real payments, run through your entire checkout flow in the sandbox. Test a successful payment, a declined card, a refund, and any other scenarios your business uses. Make sure your website correctly handles each response from the processor. Once you're confident everything works, switch your credentials from test to live and you're ready to accept real payments.
Keep your live API keys secret. Don't paste them into public code repositories, don't email them, and don't share them with anyone who doesn't need them. If you accidentally expose a key, most processors let you regenerate it when ready.
Frequently Asked Questions
Do I need a separate merchant account or does the processor handle that?
Most modern processors (Stripe, Square, PayPal) don't require a separate merchant account—they handle the acquiring and settlement for you. You just need a regular business bank account where they deposit your money. Older processors like Authorize.net sometimes require you to set up a merchant account with a bank separately, but this is becoming less common.
What if my website platform isn't listed—how do I know if I can connect a payment processor?
Check your platform's app store or integration marketplace. Most platforms have at least one payment processor integrated. If not, you can usually hire a developer to build a custom integration using the processor's API. The processor's documentation will tell you what information you need to send and what you'll receive back.
How long does it take for money to show up in my bank account?
Most processors deposit money one to three business days after the transaction. Some offer next-day payouts for a higher fee. Weekends and holidays don't count as business days. Your bank may take an additional day to post the deposit, so plan for two to four days total from payment to money in hand.
Can I accept payments without storing any customer data?
Yes. The processor stores the card data, and you only store the order information (what they bought, when, how much). You don't need to store their card number, expiration date, or CVV. For one-time purchases, you don't need to store anything except the transaction ID and the amount.
What happens if a customer disputes a charge after I've already shipped the product?
The customer's bank will contact your processor and ask for evidence that the transaction was legitimate. Keep records of the order, shipping confirmation, and delivery proof. Provide these to your processor if they ask. If you can't prove delivery or the customer claims they never received the item, you'll likely lose the dispute and the processor will reverse the charge, taking the money back from your account.