How do online payments work on a website?

Quick answer 2 min readUpdated October 18, 2026

Short answer

A website takes payments through a payment processor such as Stripe, Shopify Payments, Square or PayPal. The customer enters card details into a secure form provided by the processor, the processor checks with the card network and the bank in a second or two, and the approved money lands in your business bank account a few days later, minus a fee of roughly 2.5 to 3 per cent plus about 30 cents per transaction in Canada. Your website never stores the card number.

The pieces involved

  • Your website or store shows the product or invoice and the checkout page.
  • The payment processor (Stripe, Shopify Payments, Square, PayPal, Moneris, Helcim) provides the secure card form, talks to the card networks, handles fraud checks and pays you out. Most modern processors combine what used to be a separate 'gateway' and 'merchant account'.
  • The card networks and banks approve or decline the charge.
  • Your bank account, where payouts arrive, typically within two to seven business days, daily once established.

On Shopify, Shopify Payments is built in. On WooCommerce, you add a processor's plugin, most often Stripe or PayPal. On a custom site, the developer integrates the processor directly. In every case the sensitive part, the card entry, happens inside the processor's own secure component, which is what keeps you out of the hardest parts of card-security compliance.

What it costs

Processors in Canada typically charge around 2.7 to 2.9 per cent plus $0.30 CAD per successful online card payment, with higher rates for international cards and currency conversion. Shopify's rate depends on the plan. Interac e-Transfer and Interac Online are cheaper (often a flat fee under $1) and popular with Canadian customers, but not every processor supports Interac at checkout. There is usually no monthly fee with the big processors; traditional merchant accounts from banks may have one in exchange for lower percentages at high volume. For most small businesses a single modern processor is the right start; see the WooCommerce versus Shopify guide for a platform-by-platform breakdown of fees.

What you need before you can take payments

  • A registered business and a business bank account; processors verify both.
  • HTTPS on the site; see what an SSL certificate is. Processors will not load their forms on an insecure page.
  • Clear terms: prices, taxes, shipping, refunds and a privacy policy. Processors and card networks require these to be visible.
  • Tax handling: GST/HST and provincial taxes charged correctly by province. Shopify and WooCommerce both handle this with configuration.
  • Fraud settings: address and postal code verification, and 3-D Secure where available, reduce chargebacks.

Deposits for service businesses work the same way: an invoice or a 'pay deposit' page backed by the same processor. Ecommerce development covers stores; smaller payment features such as deposits and invoices are a common addition to a regular business site.

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