Every ecommerce site must be able to accept payments online—your business only grows when customers can check out quickly and safely. This guide breaks down the best real-world options with clear fees, strong fraud protection, and smooth checkout so you can pick a payment method that fits your tech stack and sales volume.
We researched and reviewed dozens of providers and narrowed the list to the standouts below. Whether you’re starting from scratch or upgrading an existing store, you’ll find an option that matches your products, channels, and budget.
The Best Payment Methods for Ecommerce Sites
Our favorite ecommerce payment methods are:
- Shopify – Best overall value
- Square – Best for restaurants, retail, and services
- Payment Depot – Best for high-volume sales
- Stax — Best for small businesses
- Helcim — Best for lowering fees
If you haven’t launched your store yet, Shopify is the fastest path from idea to checkout. If you already sell online—or plan to combine in-person and online sales—Square is an easy win. For higher volumes, Payment Depot or Stax can cut costs with subscription-style pricing. If you want transparent interchange-plus with no monthly fee, go with Helcim.
Shopify — Best Overall Value
Shopify gives you everything you need to sell online: payments, storefront, checkout, shipping, taxes, and marketing tools—all tightly integrated so setup is quick and maintenance stays light.
Because the core pieces are built to work together, it’s our top pick for new stores. Established brands switching platforms often do it for Shopify’s speed, reliability, and the massive app ecosystem that covers subscriptions, upsells, and internationalization.
Shopify Payments is enabled as soon as you create your store (in supported countries), so you can accept major cards and digital wallets with no separate gateway application.
All transactions, payouts, and fees appear in a unified dashboard, so reconciling sales and deposits is straightforward—no spreadsheets or manual exports needed.
With Shopify, you can accept popular payment types out of the box or via one-click wallets, including:
- Visa
- Mastercard
- American Express
- Discover
- PayPal (via integration)
- Google Pay
- Apple Pay
- Shop Pay (accelerated checkout)
Shopify Payments is included with every plan. If you choose a third-party gateway instead, Shopify charges an additional transaction fee—but there’s no extra Shopify fee when you use Shopify Payments.
There are a variety of ways to get started with Shopify.
Shopify Starter is $5 per month and lets you create shoppable links to sell via social, DMs, and email—no full storefront required.
Basic Shopify is $39 per month and includes everything you need to launch a full store. Higher-tier plans reduce processing rates and unlock more staff permissions, reports, and international features.
You can lower your website plan cost with annual billing; the Basic plan drops to $29 per month when paid yearly.
It’s a strong value for most sellers. Learn more about Shopify and start a free trial—no credit card required.
Square — Best for Restaurants, Retail, and Services
Square shines when you sell in-person and online. Its POS hardware, inventory, and staff tools sync with your online checkout, making it ideal for restaurants, retail, and service businesses that need curbside pickup, local delivery, or appointments.
Square’s ecommerce site builder is beginner-friendly and supports menus, modifiers, tips, and scheduling. If you already have a site elsewhere, use Square’s plugins to add payments in minutes.
There’s no monthly fee to take payments with Square; you pay per transaction. Online rates are competitive and transparent, and in-person processing is straightforward with Square Register, Terminal, or mobile readers.
Square integrates with popular platforms, including:
- Wix
- WooCommerce
- BigCommerce
- GoDaddy
- Ecwid
- Magento
- OpenCart
- WordPress
- WP EasyCart
- ShipStation
- Sociavore
If you’re already on one of these platforms, adding Square is painless. Click here to learn more at Square.
Payment Depot — Best for High-Volume Sales
Payment Depot is known for membership-style pricing and transparent costs. Instead of a percentage markup, you pay a flat monthly fee and a small per-transaction pass-through over interchange, which is attractive when your volume is high.
Membership plans are based on your annual processing volume, which can significantly reduce effective rates for established stores.
This model differs from flat-rate processors that take a percentage of each sale. If you’re processing meaningful volume, Payment Depot’s structure usually saves money over flat-rate pricing.
Payment Depot’s updated plans and prices include:
- Starter — $59 per month: Process up to $125,000 per year
- Starter Plus — $79 per month: Process up to $250,000 per year
- Growth — $99 per month: Process up to $500,000 per year
Per-transaction pricing uses 0% markup over interchange plus a small fixed fee (e.g., a few cents for in-person and slightly higher for online).
Need to process more than $500,000 annually? Request a custom quote tailored to your sales mix and average ticket size.
Smaller sellers may find the monthly membership doesn’t pencil out until volume grows, which is why we generally recommend Payment Depot for businesses doing at least $25,000 in monthly sales.
If you choose an annual membership, you get a 90-day money-back guarantee—cancel within the window, return any equipment, and you’ll receive a full refund.
Visit Payment Depot to lock in lower costs for heavy transaction volume. This program is available to U.S.-based companies.
Stax — Best for Small Businesses
Stax is a strong fit for small businesses that value predictable costs. You pay a flat monthly subscription with 0% markup over interchange plus a small per-transaction fee, so your effective rate improves as volume grows.
Stax accepts all major payment types, works with common POS hardware, and supports invoices, subscriptions, and card-on-file payments.
For ecommerce, you can integrate Stax with your existing cart or build a fast checkout with Stax’s templates—no coding required.
Stax’s one-click cart connects with top platforms like BigCommerce, Magento, WooCommerce, Salesforce, and others.
Stax’s ecommerce tools include:
- Unified dashboard with real-time sales and payout reporting
- Inventory sync for online and in-person sales
- Invoicing, recurring billing, and saved payment methods
- Integrations with QuickBooks and Google Business Profile
Pricing is transparent with no long-term contract. All plans include wholesale interchange pricing (0% markup), generous annual processing allowances, a knowledge base, and around-the-clock support.
Because fees don’t scale up as you sell more, high transaction counts can significantly lower your effective cost per order.
Pricing starts at $99 per month for features like ACH processing and analytics.
It’s important to note that this program is exclusively for companies based in the US. Learn more about Stax.
Helcim — Best for Lowering Fees
Helcim is an excellent one-stop option with hosted checkout pages, invoicing, and POS hardware. It’s especially appealing if you want no monthly fee and clear interchange-plus pricing with automatic volume discounts.
Helcim tailors margins based on your monthly volume and average ticket size, so higher volume typically means lower effective rates. There are also no setup, cancellation, PCI, or deposit fees, which keeps your fixed costs close to zero.
You can sell via a simple hosted checkout, add payment fields to your existing site, or use an embeddable cart. Helcim also connects with tools many businesses already use, such as QuickBooks, Drupal, and Magento.
Bottom line: Helcim is a smart pick for small to mid-sized companies processing roughly $25,000–$50,000+ per month and looking for transparent, low-friction pricing without a subscription.
Try Helcim today to see how much you can save with interchange-plus.
How to Find the Best Payment Method for Your Ecommerce Website
No two ecommerce businesses are exactly alike—your payment stack shouldn’t be either. Use the criteria below to compare options and match them to your products, average order value (AOV), and growth plans.
These are the factors we used to shortlist the providers above—use them as a checklist while you evaluate:
Fair (But Affordable) Processing Fees
Every provider charges for processing. The most common models are:
- Monthly subscription — A flat platform fee, often paired with interchange pass-through and a small per-transaction fee (e.g., Payment Depot, Stax).
- Flat-rate pricing — A single rate for all cards, simple to predict but not always the cheapest at scale (e.g., Square).
- Interchange-plus — True pass-through (interchange + provider margin), typically cheapest as volume grows (e.g., Helcim).
For example, Shopify and Square commonly charge around 2.9% + $0.30 per online transaction on entry plans. Subscription models trade a monthly fee for lower per-transaction costs. Run the math against your AOV and monthly order count to see which wins.
There’s usually a tradeoff: higher monthly fees can mean lower processing costs. If you’re just starting and volume is low, a no- or low-monthly-fee plan is often best. As you scale, subscription or interchange-plus pricing can lower your blended effective rate.
Payment Methods That Meet Your Customers Where They Live
Selling globally adds complexity—FX conversion, card acceptance by country, and local wallets. Make sure your provider supports the markets you plan to serve, including multi-currency pricing, localized checkouts, and common regional payment methods.
If international is on your roadmap, confirm how currency conversion works, whether you can settle in your home currency, and what extra cross-border or FX fees apply.
Checkout So Simple Customers Never Abandon Their Cart
Friction at checkout kills conversions. Look for:
- Accelerated wallets (Apple Pay, Google Pay, Shop Pay, PayPal)
- Guest checkout and address auto-fill
- Clear order summary (items, taxes, shipping) and total cost
- Visible, secure payment fields with strong fraud screening
Providers like Square and Shopify make checkout quick—customers can complete purchases in under a minute with saved wallets and card-on-file.
Payment Methods for Your In-Store and Online Customers
Plan to sell in person now or later? Choose a provider that unifies online and POS so inventory, reporting, and customer profiles stay in sync. That avoids double data entry and mismatched numbers.
Building your site and payments in the same ecosystem simplifies things. Shopify, Square, and Helcim all offer site or checkout builders tied directly to their payment solutions.
Shopify and Square also provide reliable POS hardware for pop-ups and brick-and-mortar locations, and they support tap, chip, and mobile payments from a phone.
Since every shopper prefers something different, aim to accept major cards plus a few popular wallets. The best gateways make it easy to turn these on without custom development.
All of the options in this guide offer competitive pricing and proven reliability. While Shopify is the most complete solution for most stores, each provider above can be the right choice depending on your sales channels, volume, and budget.