TL;DR

Shopify Payments is the right default for most standard-risk US stores, since it’s the only option with zero added Shopify transaction fees. PayPal and Stripe both work well as either your primary processor or a backup, with PayPal reaching more countries and Stripe supporting more currencies and a lower chargeback fee. If you’re in a high-risk category Shopify Payments won’t approve, Easy Pay Direct is built specifically for that, with real human underwriting instead of an algorithm that can shut your account down without warning. This guide covers what each actually costs, who should use which, and the details that only show up after you’ve already signed up somewhere.

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A lot of guides to this topic list a handful of processors, slap a star rating on each, and call it a day. That’s not especially useful once you’re actually trying to decide, since the real differences between these options live in the details.

You need to know what a processor actually costs once you add chargebacks and cross-border fees to the headline rate, how fast you’ll get paid, what happens if your account gets flagged. And, you need to know whether you can even use a given processor for the business you’re running.

Why Your Shopify Payment Processor Matters

Choosing a payment processor is one of the most important decisions you’ll make for your Shopify store. You can have great products, strong marketing, and a beautiful website, but if customers run into problems at checkout, you can still lose sales.

A payment processor does more than move money from a customer to your bank account. It affects the checkout experience, security, customer trust, and your ability to sell to shoppers around the world.

Here are some problems that can arise if you choose the wrong payment processor:

• Customers may abandon their purchase if checkout feels confusing, takes too long, or doesn’t offer their preferred payment method. Research shows that complicated checkout experiences and limited payment options are common reasons shoppers leave without buying.
• Checkout is the last step before a sale. Errors, delays, or extra friction can create a poor experience and reduce the chances that a customer will return.
• Customers need to trust your store before they enter payment information. A processor with strong security features can help protect both your business and your customers.
• If you plan to sell internationally, you’ll want support for multiple currencies and popular payment methods. Otherwise, some shoppers may decide to buy elsewhere.

The good news is that the right payment processor can:

• Help customers complete purchases with fewer obstacles.
• Support multiple payment methods, such as credit cards and digital wallets.
• Build trust through secure transactions.
• Make it easier to sell to customers in different countries.
• Integrate smoothly with Shopify so you spend less time managing payments and more time growing your business.

At the end of the day, your payment processor is a key part of the customer experience. A smooth checkout can help turn more visitors into customers and make it easier for your store to grow over time.

Top Payment Processors for Shopify

Each platform has some caveats:

• Shopify Payments isn’t available in every country, and they won’t approve many high-risk categories. See Shopify’s prohibited businesses list. 
• PayPal’s $20 chargeback fee and 21-day new-account hold can be a real cash flow problem for a brand-new store. Learn more about PayPal’s chargeback fees.
• Stripe doesn’t have the easiest setup for a non-technical owner, and their country list is narrower than PayPal’s. 
• Easy Pay Direct requires real underwriting that takes longer than instant approval. So it’s not the right fit if you need to start selling within the hour.

None of these processors can handle your VAT or sales tax obligations for you. That’s your responsibility as a merchant regardless of which processor you use. This is typically handled through Shopify’s own tax settings or a dedicated tax app rather than through your payment processor.

New accounts on any of these can face longer initial hold periods while the processor builds a track record with your store; PayPal in particular is known for a review period on new or inactive sellers that can run longer than its standard payout window. Weekend and holiday processing generally follows standard banking-day rules across all four, meaning a payout initiated Friday typically doesn’t land until the next business day.

Now, learn more about each platform. 

1. Shopify Payments

Shopify Payments is Shopify’s own native gateway. So you need no separate account and no developer setup. It can be activated directly from your Shopify admin. It supports Shop Pay, accelerated checkout, subscriptions, and Shopify POS natively.

Rates depend on your plan: Basic runs 2.9% + 30¢, Grow runs 2.7% + 30¢, and Advanced runs 2.5% + 30¢, all online. Since it’s native, there’s no added third-party gateway fee on top, which every other option on this list carries. It includes built-in fraud analysis at no extra cost and is the simplest choice for most standard-risk US stores.

2. PayPal Open

PayPal Open connects as a third-party gateway (PayPal Express), and is explicitly supported for subscription apps, with the caveat that some wallet options (Google Pay, Apple Pay) aren’t available through every subscription configuration.

The platform reaches 200+ countries and regions but supports only 25 currencies, and leans on its own wallet-based checkout rather than deep local payment method integration in most markets.

Rates vary by location and volume, with standard online checkout running around 3.49% + $0.49 in the US. New or lower-volume accounts can face a review period where funds are held before releasing to your bank, which is worth planning around if you’re just getting started rather than something to be caught off guard by.

Recommended: Add PayPal to Shopify in 10 Straightforward Steps (+Bonus Tips) 

3. Stripe

Stripe also connects as a third-party integration on Shopify, supported for subscriptions, and keeps customers on your own checkout rather than redirecting them elsewhere.

Known for a developer-friendly API and clean custom checkout integration, Stripe runs around 2.9% + 30¢ online in the US, with broader currency support (135+) than PayPal, though a narrower list of supported countries (46-47). 

It’s a strong fit if you want more control over checkout customization, and a steeper learning curve if you’re not working with a developer.

4. Easy Pay Direct

Easy Pay Direct isn’t a native Shopify payment gateway; it typically connects through a supported gateway integration rather than a one-click activation, and setup involves submitting your business for underwriting first, which takes longer than connecting PayPal or Stripe.

It’s built specifically for stores other processors won’t approve: high-risk categories, or accounts that have already been flagged or shut down elsewhere. Rather than one flat advertised rate, pricing is quoted per merchant and vertical, using interchange-plus, tiered, or flat-rate models depending on your business, with online rates generally starting in the 2.4%-2.7% range plus a per-transaction fee, a roughly $99 setup fee, and a monthly fee typically in the $25 to $36 range. 

The real difference isn’t the pricing structure, though. It’s that Easy Pay Direct underwrites your account with an actual person reviewing your business before approval, which tends to mean more account stability once you’re in, in exchange for a setup that takes a few days instead of a few minutes.

Start processing high-risk Shopify payments with Easy Pay Direct today →

Be Sure to Calculate Real Costs – Not Just Headline Rates

The rate on a processor’s homepage is rarely the whole story. There are a few layers worth knowing:

Using any processor other than Shopify Payments adds Shopify’s own surcharge on top of that processor’s rate: 2.0% on the Basic plan, 1.0% on Grow, 0.6% on Advanced. This is the single most commonly overlooked cost in this whole comparison, since it’s a Shopify fee, not something the processor itself charges or discloses.

Covered in detail below, but worth flagging here: these range from $15 to $20 depending on processor and how the dispute is filed, and they’re easy to forget when comparing headline transaction rates.

Both PayPal and Stripe charge roughly 1.5% extra on international transactions, with Stripe splitting that into a cross-border fee plus a separate currency conversion fee when both apply.

Shopify Payments, PayPal, and Stripe all use flat-rate pricing: one advertised percentage plus a fixed fee, regardless of the card used. Easy Pay Direct uses interchange-plus pricing instead, meaning you pay the card network’s actual interchange rate plus a transparent markup. Flat-rate is simpler to predict; interchange-plus is often cheaper at real volume, since you’re not subsidizing a blended average rate on every transaction.

Say your store does $10,000/month at a $60 average order, roughly 167 transactions. On Shopify Payments Basic (2.9% + 30¢), that’s about $340 in processing fees for the month. Route the same volume through Stripe instead, and you’d pay Stripe’s 2.9% + 30¢ (roughly the same $340) plus Shopify’s third-party charge of 2.0% (~$200 more). In that case, processing fees would land around $540 total, which is a significant difference that “Stripe charges 2.9%” never shows you.

Don’t Forget Chargebacks, Disputes, & Account Stability

The “PayPal and Stripe shut down my accounts” narrative you see across the internet is real, but incomplete. Algorithmic processors can flag and freeze an account based on automated risk signals. Sometimes sellers get limited notice and limited explanation, since there’s no dedicated underwriter reviewing your specific file. 

A dedicated merchant account, the kind Easy Pay Direct provides, is placed with a bank that has already reviewed and accepted your business model, which generally equates to more stability once you’re approved, in exchange for a slower approval process upfront. Neither approach is categorically safer; they trade speed for review depth in opposite directions.

Shopify Payments includes built-in fraud analysis at no extra cost. PayPal and Stripe both include baseline fraud screening, with more advanced tools (like Stripe Radar’s custom rules) available as paid add-ons at higher usage tiers. Easy Pay Direct’s fraud and chargeback monitoring is typically built into the underwriting and account setup itself, tailored to your specific vertical’s risk patterns.

For added fraud support, consider a dispute management platform like Chargeflow or Disputifier.

Learn more: Shopify Chargebacks: How to Avoid & Manage Payment Reversals 

Do You Need to Accept Non-Credit Card Payment Methods?

Offering a wallet option like Apple Pay or Shop Pay generally improves mobile conversion, since it removes manual card entry at checkout, though the exact lift varies by store and audience. If BNPL matters to your customers specifically, that’s a dedicated Shopify app layer (Klarna, Afterpay) in most setups rather than a built-in feature of any single processor here.

How to Switch Processors Without Breaking Everything

If you’re changing processors on an existing Shopify store:

• Saved cards don’t transfer. 
• Active subscriptions need a plan. 
• Test before you fully switch. 
• Expect a short overlap, not a hard cutover, 

So, customers with a card saved through your old processor’s wallet (like PayPal’s saved payment method) will need to re-enter payment details with the new one. And, recurring billing tied to your old processor doesn’t automatically move; check whether your subscription app supports a migration path, since some do and some require manually re-subscribing customers.

Be sure to run real test transactions through the new processor in a low-stakes way before routing your full checkout through it, so you catch configuration issues before a customer does.

Many stores run both processors active briefly during a transition rather than flipping a single switch at a specific moment, reducing the risk of a failed checkout during the changeover itself.

Final Thoughts

There’s no single best payment processor for every Shopify store, despite how most “top 5” lists are written. If you’re in a high-risk category and tired of algorithmic shutdowns, Easy Pay Direct is worth a look. 

The right choice depends on your risk category, your international footprint, and how much you value a fast automated setup against the stability of a dedicated account that’s actually been reviewed by a person. Run the real total cost, including Shopify’s own layered fees, against your actual numbers before deciding, not just the headline rate on a provider’s homepage.

To ideate, plan, and launch a new Shopify store or product, claim your free online launch dashboard today.

Frequently Asked Questions About Shopify Payment Processors