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Payment processing for ecommerce businesses, from cart to settlement

Payment processing for ecommerce businesses means taking cards at your online checkout, renewing subscribe-and-save orders, collecting phone and custom orders by payment link, and handling refunds and chargebacks. RapidCents runs checkout through Hosted Checkout or its Payment Gateway API, bills renewals with Recurring Payments, handles chargebacks in Disputes, and works with Shopify, WooCommerce and BigCommerce through RapidBridge.

Ecommerce team reviewing online order payments in the RapidCents dashboard, with a card terminal on the desk
An online store's team checks the day's orders, refunds and settlement in the RapidCents dashboard, with a card terminal on the desk for in-person sales.
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  • SOC 2 Type II
  • All major cards: Visa, Mastercard, Amex, Discover, UnionPay, Diners Club & Interac Debit
  • Interchange-plus available
  • Canadian support

How ecommerce businesses get paid

Ecommerce businesses get paid in six ways: card orders at the storefront checkout, subscription and subscribe-and-save renewals, phone and custom orders taken outside the cart, pre-orders and made-to-order deposits, wholesale invoices, and sales at pop-ups or a showroom. Put your order or invoice number on every payment so finance can match it. Orders placed on marketplaces such as Amazon or Etsy are collected and paid out by the marketplace instead.

  • Card orders at your storefront checkout

    A shopper pays the moment they place an order in your cart. The card is authorized at checkout through Hosted Checkout or the Payment Gateway, and physical goods are usually captured when they ship. If the card is declined, or the shopper does not finish a 3D Secure check, they can try again without rebuilding the cart. Finance gets a transaction ID tied to the order number.

  • Subscription and subscribe-and-save renewals

    A subscriber pays on a schedule for replenishment orders, a subscription box or a paid membership. Recurring Payments charges the saved card each cycle, which needs the customer's authorization for the amount, the timing and how to cancel. If a card has expired or been replaced, automated retries and Account Updater pick up the new details. Finance gets one payment per cycle, linked to the subscription and the shipment it paid for.

  • Phone, chat and custom orders outside the cart

    A customer who wants an engraved item, a custom size or a bulk quantity orders by phone, chat or email instead of the cart. Your team sends a Payment Link by email or SMS, or keys the card into the Virtual Terminal, which checks AVS and CVV. If the billing address does not match the card, you sort it out before shipping. Finance gets a payment carrying the draft order or quote number.

  • Pre-orders, backorders and made-to-order deposits

    A shopper pays in advance for an item that ships weeks later: a pre-order, a backordered product or a made-to-order piece. You can charge a deposit at checkout and collect the balance with a Payment Link when the item is ready. If the wait is long, remember that an authorization held without capture can expire before the item ships. Finance gets the deposit and the balance as two payments under one order.

  • Wholesale orders from retail stockists

    A boutique or retailer that stocks your products pays a wholesale invoice rather than checking out. Invoicing sends a branded invoice with a payment link, and the stockist pays by card, or by bank payment where your account offers it. If a stockist pays in part or after the due date, the invoice shows its status until it is settled. Every payment carries the invoice number.

  • Pop-up, market and showroom sales

    Shoppers who meet your brand at a market stall, a pop-up or a showroom pay in person by chip or contactless on a RapidCents mobile terminal, or by tapping a card on a supported iPhone or Android phone with Tap to Pay. A card that will not tap can be inserted instead. Finance gets in-person sales in the same reporting as online orders, so revenue from both channels reconciles in one place.

Online store payment gateway: how checkout runs from cart to capture

An online store payment gateway takes the card at checkout, gets the shopper's bank to approve it, confirms the order to your store, and captures the funds when you ship. With RapidCents, you either send shoppers to Hosted Checkout, a payment page in your branding that you redirect to or embed, or build checkout on the Payment Gateway's REST API, which authorizes, captures, voids, refunds and tokenizes cards and reports each result by webhook.

  • From cart to confirmed order

    The shopper fills the cart and reaches payment. Hosted Checkout or your own payment form sends the card to RapidCents for authorization, and a webhook tells your store the result, so the order is confirmed only after approval. An idempotency key on each request stops a double-clicked Pay button from charging twice. When the parcel ships, you capture the authorization; if the order is called off before then, you void it and nothing settles.

  • Decide these before the first live order

    Choose when each product type is captured: digital downloads and gift cards right away, physical goods at shipment. Set Fraud Prevention rules and 3D Secure for card-not-present orders, put your order number in the payment reference, and point webhooks at the system that updates order status. Then place test orders that cover an approval, a decline, a void and a refund before real shoppers reach the page.

  • Abandoned checkout payment declines

    A decline at checkout loses a shopper who had already chosen to buy, and the structured error code the gateway returns tells you which kind of decline it was. Show the shopper a plain message and keep the cart intact, so trying another card takes seconds rather than a rebuilt order. A burst of small declined orders from new accounts usually signals card testing, which Fraud Prevention rules and your storefront's bot protection are there to stop.

  • Chargebacks after delivery

    Online orders draw two main kinds of chargeback: item not received, and not as described, including the customer who keeps the product and disputes the charge anyway. Disputes in RapidCents shows each chargeback with its reason and response deadline, and you answer with the tracking number, delivery confirmation, product page and the return policy the shopper accepted. A prompt refund on a genuine return can head off a dispute before it starts.

  • A $180 dinnerware set, voided instead of refunded

    Say a store selling handmade ceramics takes a $180 order for a dinnerware set, authorized at checkout with the order number in the payment reference. A kiln fault means the set cannot ship for a month, and the customer decides not to wait. Because the payment was never captured, the team voids the authorization instead of refunding it: the charge never settles, and there is no refund to reconcile later.

Shopify payment processor alternatives: which payments can move

A Shopify store has three realistic alternatives to Shopify Payments: a third-party provider that Shopify lists for your country, a different storefront platform where you choose the gateway, or keeping Shopify Payments at checkout and moving only the payments taken outside the cart to another processor. Depending on your plan, Shopify may charge its own transaction fee on orders a third-party provider processes, so weigh that fee alongside any processing difference.

  • How each alternative works

    Inside Shopify checkout, a third-party card provider replaces Shopify Payments for card orders, and Shopify generally runs one card provider at a time. On a platform such as WooCommerce or Adobe Commerce, the gateway is your choice, connected through a plugin or your own code. The third route leaves checkout alone: phone, custom and wholesale orders are paid by RapidCents Payment Link, Invoicing or Virtual Terminal, and the payment reference is recorded on the Shopify order.

  • Check these first

    Find your Shopify plan and whether it adds a transaction fee for outside providers, then look at the payment providers Shopify offers for your store's country. List your order types: checkout orders, draft orders, subscriptions run by a subscription app, and wholesale. Check whether that subscription app works with any provider other than Shopify Payments. Then talk to your RapidCents representative, who will walk you through which of the three routes fits your plan and country.

  • What goes wrong with two processors

    Running Shopify Payments for checkout and RapidCents for off-cart orders means two settlement reports and two places where chargebacks arrive. Refunds must go back through the processor that took the payment: for an order paid by RapidCents link, refunding it in Shopify only records the refund, and the money is returned in RapidCents against the original transaction. Tag each order with the processor that collected it, so returns staff know where to refund.

  • A $2,400 sofa: deposit first, balance later

    Say a furniture brand on Shopify keeps Shopify Payments for cart orders but sells custom upholstery by phone. The team builds a draft order for a $2,400 sofa, sends a RapidCents Payment Link for the deposit and records the link's transaction ID on the order. When the sofa is ready, a second link collects the balance. Both payments reconcile to the draft order number in RapidCents reporting, separately from the checkout sales Shopify settles.

RapidCents products for ecommerce businesses

Hosted Checkout and the Payment Gateway cover the storefront checkout, from a branded payment page you redirect to or embed, to a checkout your developers build on the REST API. Recurring Payments renews subscription and subscribe-and-save orders with retries and card updates, and Disputes tracks chargeback reasons, deadlines and delivery evidence.

How does a multi-currency ecommerce checkout work?

A multi-currency ecommerce checkout shows shoppers abroad prices in a currency they recognize, while the currency the card is charged in, and the currency you are paid in, are set by your merchant account rather than the storefront. RapidCents accepts cards issued in other countries through International Payments. Your RapidCents representative will tell you which charge and settlement currencies your account supports before you price in a second currency.

  • Displayed price, charged currency, settlement currency

    One order can involve three currencies. The display currency is what the shopper sees, often converted by a storefront setting or plugin. The charge currency is what the card is actually billed in; when that is your account currency, the shopper's own bank converts the amount and may add a foreign transaction fee. The settlement currency is what reaches your bank account. Mixing these up is how a shopper ends up disputing an amount they did not expect.

  • Set up before you sell abroad

    Pick the countries you will ship to, then ask your RapidCents representative which currencies your account can charge and settle in. Say on the checkout page which currency the card will be charged in, and make sure the business name on the shopper's card statement is one they will recognize. Set 3D Secure and Fraud Prevention rules for foreign-issued cards, and record the charge currency beside the order number so finance reads each payment correctly.

  • Refunds, exchange rates and foreign declines

    A refund goes back in the currency of the original charge, against the original transaction. If the shopper's bank converted the charge, the amount they get back in their own currency can differ from what they paid, because rates move between purchase and refund; say so in your return policy. Issuers abroad also apply their own fraud rules to foreign merchants, so review decline codes by card country before loosening your rules.

  • A $95 order returned from Australia

    Say a skincare brand that sells mostly at home ships a $95 order to a customer in Australia. The storefront shows the price converted for the shopper, the card is charged in the store's account currency, and the shopper's bank converts it. Two weeks later the customer returns one serum. The refund goes back in the account currency against the original transaction, and the shopper's bank converts it at that day's rate.

What drives payment processing fees for ecommerce businesses?

Payment processing fees for ecommerce businesses are driven mainly by interchange on card-not-present orders, which the card networks set by card type, plus your RapidCents markup and any fees for equipment or services. RapidCents prices on interchange-plus: interchange passes through at cost, your markup is set out in your Fee Schedule, and the agreement is month to month with no fixed term, so your cost follows your own order mix.

  • Why online orders price differently

    Every checkout order, payment link and keyed phone order is card-not-present, and interchange for those transactions sits in different categories from cards tapped or inserted at a terminal, usually at a higher level. Within that, a premium rewards card or a corporate card carries different interchange from a standard debit or credit card, and cards issued abroad add cross-border network costs. Your statement shows the mix your shoppers actually bring.

  • Keep platform fees and processing fees apart

    An online store pays at least two parties: the storefront platform, for its subscription, apps and any transaction fee it charges when an outside provider takes the payment, and the processor, for interchange, markup and services. Comparing only the processing quote can hide a platform fee that appears once you switch, so line the two up per order before deciding.

  • Refunds, chargebacks and other exceptions

    Returns are routine in ecommerce, so ask any provider how a refund is priced and whether interchange on the original sale comes back. Ask the same about chargebacks and dispute fees, 3D Secure and cross-border orders, and have each answer shown on a sample statement. A quote that covers only a clean domestic sale describes a store you do not run.

  • What to bring to compare

    Bring three recent statements, your average order value, your split of debit, credit, premium and corporate cards if you know it, the share of orders paid with foreign cards, subscription versus one-time volume, and your monthly refunds and chargebacks. Upload a statement to Fee Check to see interchange separated from markup, then ask every provider for a written, itemized quote priced on that same month.

Shopify, WooCommerce and other platforms: compatibility and data flow

Shopify payment processor compatibility, like compatibility with any storefront platform, comes down to three routes: inside the platform's checkout, through a plugin or API integration you control, or by payment link outside the checkout. RapidCents integrates with many major platforms through APPIE and RapidBridge, and RapidBridge works with Shopify, WooCommerce, BigCommerce and Adobe Commerce. Your RapidCents representative will walk you through the option that fits your platform and version.

  • Shopify

    Shopify hosts your storefront and its checkout, and RapidBridge works with Shopify, so RapidCents payments connect to the store you already run. Orders paid by other means, such as a phone order paid by Payment Link, can be marked as paid by hand. Your RapidCents representative will show you which events, such as capture, refund and chargeback, reach the Shopify order for your plan and country.

  • WooCommerce

    WooCommerce adds a store to a WordPress site, and WooCommerce credit card processing runs through whichever payment plugin you install, which gives you more say over the gateway than a hosted platform does. RapidBridge works with WooCommerce, and a developer can also connect Hosted Checkout or the Payment Gateway API and map webhooks to order status. Refunds started on the order screen go back to the original transaction.

  • BigCommerce

    BigCommerce hosts the storefront and offers payment providers chosen in the store's payment settings. RapidBridge works with BigCommerce, so authorize, capture and refund move between your store and RapidCents without changing the software. Settlement data reaches your books through the QuickBooks Online and Xero connections, and orders taken outside the BigCommerce checkout can be collected with payment links and invoices.

  • Adobe Commerce

    Adobe Commerce, built on Magento, is usually run by a development team, and RapidBridge works with Adobe Commerce (Magento) so RapidCents payments run inside the store you already have. If your team prefers to build, an API integration with the Payment Gateway is a realistic route, with the module maintained through platform upgrades. Your representative will walk you through which payment events your order management needs returned.

  • Wix eCommerce

    Wix eCommerce runs checkout inside a Wix site and accepts payments through Wix Payments or the third-party providers Wix supports in your country. RapidCents integrates with many major platforms through APPIE and RapidBridge; the right option depends on your Wix plan and country, and your representative will walk you through it. Custom and wholesale orders can be collected with RapidCents invoices or payment links outside the Wix checkout, with the transaction ID added to the order for reconciliation.

Payment options for ecommerce businesses in Canada

Online stores in Canada take Visa, Mastercard and American Express at checkout, accept co-badged Visa Debit and Debit Mastercard cards online where those networks are enabled, and can collect wholesale invoices or subscription payments by EFT or pre-authorized debit (PAD) where bank payments are enabled. Interac debit is for in-person sales on a RapidCents terminal. Payments settle in CAD.

  • Debit online and at the pop-up

    At an online checkout, a debit card is accepted when it carries a Visa Debit or Debit Mastercard logo and those networks are enabled on your account. Interac debit, inserted with a PIN or tapped, is a terminal payment: offer it at markets, pop-ups and a showroom counter on a RapidCents terminal, so local shoppers can pay by debit in person.

  • EFT and PAD for stockists and subscribers

    Retail stockists can pay wholesale invoices by EFT, and subscribers can pay for a monthly box by pre-authorized debit once they sign a PAD agreement, where these bank payments are enabled on your account. Put the invoice or subscription number on each payment so it matches the order in your storefront and the deposit in your books.

  • GST/HST and provincial tax on receipts

    Your storefront's tax settings work out GST/HST, and provincial sales tax where it applies, based on where each order ships, and the total appears on the receipt. Card processing carries that total; it does not calculate, file or remit tax, so registration questions about selling into other provinces stay with your accountant.

Switching processors without breaking open orders, renewals or refunds

Switching an online store's processor works best as a staged move: list everything that still depends on the old processor, test the new checkout, move order types one at a time, and reconcile the first settlements line by line. Open authorizations, refunds on past orders and saved cards for subscriptions stay with the old processor until they settle, are refunded or are replaced, so keep that account open while they wind down.

  • List what depends on the old processor

    Before you move, list uncaptured authorizations on unshipped orders, orders still inside your return window, subscriptions running on saved cards, unpaid invoices and payment links, and open chargebacks. Each one stays with the processor that created it: a refund on last month's order goes back through the old account, and an open dispute is answered there. Export transaction and settlement history so finance can still trace past orders.

  • Saved cards and subscribers

    Saved cards move between processors only when both providers agree to a secure transfer, and that is never automatic, so ask both before you plan around it. If a transfer is not possible, subscribers enter their card on a RapidCents payment page at or before their next renewal. Tell them in advance, and keep their authorization for the amount, timing and cancellation terms on record for the new schedule.

  • Test, then move traffic in stages

    Once your account is approved, run a sale, a void, a refund, a decline and a webhook through the new setup before real shoppers see it. Then move one order type first, such as phone orders by Payment Link, and keep the old account open until the new setup has been through a full return cycle. Watch approval and decline codes for the first weeks, especially on foreign cards and renewals.

  • Reconcile settlements to orders and the ledger

    Put your order number and the RapidCents transaction ID on every payment, then compare each settlement deposit with the orders, refunds and fees in the settlement report, exported as CSV or PDF. Settled transactions, fees and refunds connect to QuickBooks Online and Xero, and larger ERPs such as NetSuite and SAP import settlement files. Your representative will line this up with your accounting edition.

Payment questions from ecommerce businesses

What is the best payment processor for ecommerce businesses?

The best payment processor for an ecommerce business is the one that fits your platform, order types and card mix, not the one at the top of a ranking. Check whether each provider can run inside your platform's checkout or only beside it; how it handles capture at shipment, declines, refunds and chargebacks; whether it supports saved cards and renewals with customer consent; how its pricing is itemized; and whether there is a fixed term. Ask RapidCents and each shortlisted provider to run a test order, a partial refund and a failed renewal, then compare written quotes priced on the same statement.

How much does credit card processing cost for ecommerce businesses?

There is no single price: the cost of credit card processing for ecommerce businesses depends on the cards your shoppers use and how each payment is taken. Under RapidCents interchange-plus pricing, you pay interchange at cost, set by the card networks and usually higher for card-not-present orders than for tapped cards, plus the RapidCents markup in your Fee Schedule and fees for equipment or services, if applicable. Platform subscriptions and platform transaction fees are separate. For an itemized quote, bring recent statements, or upload one to Fee Check to see interchange and markup apart.

Can Shopify use a different payment processor?

Yes, within limits. A Shopify store takes cards at checkout through Shopify Payments or through a third-party provider from the list Shopify shows for your country, and Shopify may add its own transaction fee to third-party orders, depending on your plan. RapidBridge works with Shopify, and your RapidCents representative will walk you through the option that fits your plan and country. Payments taken outside the checkout, such as phone, custom and wholesale orders, can be collected with RapidCents Payment Links or Invoicing and recorded on the Shopify order.

How can an ecommerce business switch processors without losing payment history?

You keep payment history by exporting it and keeping the old account open, not by moving it. Download transaction, refund, chargeback and settlement reports from the old processor for as far back as your accountant needs, and keep access while refunds and disputes on past orders are still possible, since those go back through the processor that took the payment. Saved cards move only if both processors agree to a secure transfer. Record on each order which processor collected it, so history stays traceable from the order screen.

Which payment options can an ecommerce business in Canada offer?

Card payments online, Interac debit in person, and bank payments where your account has them enabled. Shoppers can pay at checkout with Visa, Mastercard and American Express credit cards and with co-badged Visa Debit or Debit Mastercard cards. At pop-ups and showrooms, Interac debit works by chip and PIN or contactless on a RapidCents terminal. Stockists and subscribers can pay by EFT, or by PAD with a signed agreement, and payments settle in CAD. Your RapidCents representative will tell you which methods your account has.

How can we use another payment gateway with our ecommerce platform?

Use the route your platform allows: a provider you can select inside the platform's checkout, a plugin or API integration you control, or payment links for orders taken outside the checkout. RapidBridge works with Shopify, WooCommerce, BigCommerce and Adobe Commerce, and on a custom storefront a developer can connect Hosted Checkout or the Payment Gateway API and map webhooks to order status. The platform keeps the cart, products, tax and order status; the gateway authorizes, captures and refunds. Your RapidCents representative will walk you through your route.

How can we accept cards in more than one currency?

You can accept cards issued in other countries through RapidCents International Payments, and whether you can also charge in more than one currency depends on what your merchant account supports. Your storefront can display converted prices, but the charge and settlement currencies are set by the account, so ask your RapidCents representative which ones yours supports before pricing in a second currency. When cards are charged in your account currency, the shopper's bank converts the amount. Refunds return in the original charge currency against the original transaction, so the shopper's converted refund can differ from the converted charge.

How can we recover customers whose checkout payment fails?

Read the decline reason, then give the shopper a fast way to pay for the same order. A soft decline, such as a mistyped expiry date or an unfinished 3D Secure check, often succeeds on a retry; a hard decline, such as a closed account or a lost-card flag, needs a different card. If the shopper has left, your team can send a RapidCents Payment Link for the order total by email or SMS and mark the order paid with the link's reference. Limit retries per order, because rapid repeated attempts look like card testing.

How can we connect online refunds to the original order?

Refund against the original transaction, never as a separate payment, and carry the order number on both. With RapidCents, a refund through the Payment Gateway references the original transaction, so the order number, the charge and the refund appear together in transaction and settlement reports. If the order has not been captured yet, void the authorization instead and nothing settles. For a partial return, refund only the returned items. Your storefront records the return, restock and exchange; RapidCents moves the money and reports it.

How can we compare gateway fees with platform transaction fees?

Compare the total cost per order under each setup, because platform charges and processing charges arrive on different invoices. On the platform side, add the subscription, any transaction fee the platform charges when an outside provider takes the payment, and payment-related app fees. On the processing side, take interchange, markup and fees for equipment or services, if applicable, from a real statement. Run both sides over the same month of orders, refunds and chargebacks. Fee Check separates interchange from markup on an uploaded statement; your platform invoice supplies the rest.

What MCC is used for ecommerce businesses?

MCC 5399, miscellaneous general merchandise, is commonly associated with online stores that sell a broad mix of goods. The code describes what you sell, not the fact that you sell online, so a store focused on one category may be classified under that category's code instead, while online orders are flagged as card-not-present on each transaction. Your RapidCents representative will set the right merchant category based on what your business actually sells.

Industries with similar online payment workflows

Digital Products and Downloadable Software run the same checkout and chargeback evidence without the shipping step, Software & SaaS and Edtech & eLearning rely on the renewals and failed-payment recovery behind subscribe-and-save, and Gaming shares the web checkout and card-testing risk every online store manages.

See all industries

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