Choosing a Payment Processor for Your Shopify Store

What "best" means depends on your sales volume, product type, and where your customers are

There is no single best payment processor for Shopify because the right choice depends on your specific situation. A processor that works well for a clothing store selling $5,000 a month to US customers may cost you money if you're selling digital products internationally or processing $50,000 a month. The main variables are your monthly sales volume, whether you sell physical goods or digital products, which countries your customers are in, and how much you're willing to pay in fees.

Shopify's own payment processor, Shopify Payments, is built into your store and has no setup fees or monthly minimums. Stripe, Square, PayPal, and Authorize.Net are also common choices that connect to Shopify. Each charges different rates for credit card processing, and some add extra fees for international sales, refunds, or chargebacks. Before you choose, you need to know your actual transaction volume and whether you'll be taking payments outside the United States.

Key Takeaways

• Shopify Payments has no setup or monthly fees and is the simplest to set up, but is only available in certain countries and may not be the cheapest option at high sales volumes.
• Stripe and Square both charge per-transaction fees with no monthly minimums, making them predictable for small stores but potentially expensive as you scale.
• Your total cost depends on your sales volume, the percentage of international transactions, and how often customers request refunds or chargebacks.
• You can change processors later, though switching requires notifying customers and updating payment settings, so test your choice on a small scale first if possible.

Shopify Payments: Built-in, simple, but not available everywhere

Shopify Payments is Shopify's own processor and is the default option when you create a store. It charges a percentage of each transaction (the rate varies by country and card type, typically 2.2% to 2.9% plus a fixed fee per transaction) with no setup fee, no monthly fee, and no separate account to open. The money lands in your bank account within one to two business days. You see transaction details directly in your Shopify dashboard.

The catch is that Shopify Payments is not available in all countries. It works in the United States, Canada, the United Kingdom, Australia, and several others, but not everywhere. If you're outside a supported country, you must use a third-party processor. Even if you're in a supported country, Shopify Payments may not be the cheapest option if you process a very high volume of transactions or if most of your sales are international.

Stripe: Per-transaction fees, no minimums, widely available

Stripe charges a percentage plus a fixed amount per successful transaction (typically 2.9% plus 30 cents in the US, with different rates in other countries). There are no setup fees, no monthly minimums, and no hidden charges for refunds or chargebacks—those are included in the per-transaction cost. Stripe is available in over 40 countries and handles international payments well, though the percentage varies by country.

Stripe's main advantage is predictability: you know exactly what you'll pay per transaction, and the cost scales with your sales. If you process $1,000 a month, you pay roughly $30 in fees. If you process $10,000 a month, you pay roughly $300. The downside is that at very high volumes, the per-transaction model can become expensive compared to a processor that offers volume discounts or tiered pricing.

Square: Similar to Stripe, with in-person payment options

Square charges the same per-transaction rate as Stripe in most cases (2.9% plus 30 cents in the US) and also has no setup or monthly fees. Square's main difference is that it also offers in-person payment processing through Square hardware, which can be useful if you sell both online and at markets or pop-ups. The online payment processing itself works the same way as Stripe.

Square is available in the US, Canada, Australia, Japan, and a few other countries, but not as widely as Stripe. If you only sell online and don't need in-person payments, Stripe and Square will cost you roughly the same. Choose Square if you think you'll add in-person sales later or if you prefer their dashboard layout.

PayPal: Familiar to customers, but higher fees and slower payouts

PayPal charges 2.2% plus 30 cents per transaction in the US for standard credit card processing through Shopify, which is lower than Stripe or Square. However, PayPal also charges a fee for refunds (the transaction fee is not refunded to you), and payouts can take up to two business days. PayPal is available in most countries and is recognizable to many customers, which can reduce cart abandonment.

The trade-off is that PayPal's interface is less integrated into Shopify than Shopify Payments or Stripe, and customer support can be slower. If your customers strongly prefer PayPal or if you already have a PayPal business account, it can be a reasonable choice. But for most new stores, Stripe or Shopify Payments will give you a better experience.

Authorize.Net: Older system, useful if you have existing contracts

Authorize.Net is an older payment processor that charges a setup fee, a monthly fee, and a per-transaction fee. The total cost is higher than Stripe or Shopify Payments for most small stores. However, some businesses already have Authorize.Net accounts from before they moved to Shopify, and switching processors can be disruptive. If you already have an Authorize.Net contract and your volume is low, it may not be worth switching.

If you're starting fresh, Authorize.Net is not a good choice. The combination of setup, monthly, and per-transaction fees makes it expensive compared to modern processors that charge only per transaction.

How to compare costs for your actual situation

To find the cheapest processor for you, calculate what you'd pay under each option using your actual monthly sales and transaction mix. For example, if you process $5,000 a month in US credit card sales, Shopify Payments might cost you $110 to $145, while Stripe would cost roughly $145 to $175. At $50,000 a month, the gap widens because Shopify Payments' percentage-based fee compounds.

If you sell internationally, add the international transaction fee to your calculation. Shopify Payments charges an extra 1% for international cards. Stripe charges a different percentage depending on the card's country of origin. PayPal also charges extra for international transactions. For a store that's 20% international sales, this can add $20 to $50 a month to your bill.

Write down the three processors you're considering, plug in your monthly volume and your international percentage, and calculate the total fee for each. The difference is usually between $10 and $100 a month for small stores—not huge, but worth knowing before you commit.

Switching processors later is possible but requires planning

You can change payment processors after you've launched, but it requires a few steps. You'll need to update your Shopify payment settings, which takes a few minutes. If you've set up automatic billing for subscriptions or recurring charges, you'll need to notify customers and have them re-enter their payment information. For one-time purchases, the switch is seamless—old orders stay in your history, and new orders use the new processor.

Because switching has some friction, it's worth testing your processor choice on a small scale first. If you're unsure between Stripe and Shopify Payments, start with Shopify Payments (it's the default), process a few hundred dollars in sales, and see how the experience feels. If you want to switch, you can do it in a few minutes. This approach lets you learn which processor works best for your workflow without committing upfront.

Frequently Asked Questions

Can I use multiple payment processors at the same time?

Yes. You can offer Shopify Payments and Stripe simultaneously, for example, and let customers choose which one to use at checkout. This is useful if you want to test a new processor or if your customers have strong preferences. However, most stores use only one processor to keep the checkout experience simple.

What happens to my transaction history if I switch processors?

Your transaction history stays in Shopify and is not affected by switching processors. Old orders remain visible in your dashboard with their original payment method. New orders will show the new processor. You can view and refund old transactions through Shopify's history, even after you've switched.

Do I need a separate bank account for each processor?

No. All processors can deposit funds into the same bank account. You'll see deposits from each processor separately in your bank statement, but they go to one account. You can change which account receives deposits at any time through the processor's settings.

Which processor is cheapest for selling digital products?

For digital products, the per-transaction fee is the same across processors, so cost depends only on volume. Shopify Payments and Stripe are both good choices. Some stores prefer Stripe for digital products because it integrates well with fulfillment automation, but the fee difference is negligible.

What if my processor declines a transaction or flags it as fraud?

Each processor has its own fraud detection system, and they sometimes disagree on what's risky. If you find that one processor is declining too many legitimate transactions, switching to another can help. Stripe and Shopify Payments tend to have different fraud thresholds, so testing both can reveal which one works better for your customer base.