Shopify Payments Review – What I’ve Learned from 10+ Years Using It

If you’re running a Shopify store, using Shopify Payments is a no-brainer – as long as you’re in a supported country.

It cuts out third-party fees, simplifies payouts, and ties directly into your dashboard.

After over a decade in ecommerce, and having worked with stores of all sizes, I can confidently say Shopify Payments has made life easier for most of the brands I work with.

But it’s not perfect. There are limits, especially for international sellers or those in high-risk industries.

Below, I’ll walk you through everything you need to know – from setup to fees to how it stacks up against Stripe and PayPal.

Shopify Payments: Quick Pros & Cons Summary

Why I Use Shopify Payments (and Still Do)

I’ve used Stripe, PayPal, Klarna, and even obscure gateways like Authorize.net. When Shopify Payments came on the scene, I didn’t think much of it.

I assumed it was another basic built-in option meant for beginners. But after testing it across multiple stores over the last few years, I started recommending it more often—and for good reason.

The real benefit became obvious when managing stores with a higher volume of orders and multiple staff. Payment systems can become a point of friction if they don’t sync well with your operations.

Shopify Payments avoids that by removing extra steps, reducing manual tracking, and keeping everything under one roof.

Here’s what’s kept me using it on my own stores and those I manage:

• Integrated Tracking:
  Payments, refunds, disputes, and order status are all in one dashboard. There’s no need to log into another tool. I can pull up any order, check the customer’s payment status, and issue a refund in seconds.
• No More Third-Party Fees:
  If you use Stripe or PayPal on Shopify, you’ll get hit with an additional fee from Shopify itself. This ranges from 0.5 to 2 percent depending on your plan. With Shopify Payments, that fee disappears entirely.
• Faster Payouts:
  Once your account is verified, payouts are smooth and predictable. In the US, I usually see funds hit within 1 to 2 business days. That’s crucial for cash flow, especially during product launches or holiday periods.
• Better Checkout Experience:
  Customers can use Apple Pay, Shop Pay, and Google Pay without switching tabs or entering their details manually. This frictionless flow has a noticeable impact on conversion rates.

If you’re scaling or even just getting started, Shopify Payments removes a layer of tech setup.

You don’t need to install a separate payment gateway, configure webhooks, or monitor separate payout logs. It just works.

To give you a clearer comparison, here’s how it stacks up against third-party options:

What this means in practice is less time spent troubleshooting payment issues, fewer customer complaints, and a smoother experience for everyone involved.

It doesn’t matter if you’re just starting or scaling.

The native integration with the rest of the Shopify ecosystem makes it the best choice for most merchants, especially those who want a clean, low-maintenance solution without sacrificing features or control.

Setup: Getting Started Is Fast, but Watch for Verification Delays

Activating Shopify Payments is one of the easiest onboarding experiences I’ve had with a payment processor. It’s quick, intuitive, and directly accessible from the Shopify admin.

There’s no need to sign up through a third-party gateway or mess with API keys. But while the process itself is streamlined, your experience may vary depending on where you’re based and what you sell.

Most stores can get approved in under an hour. Others may get flagged and put into manual review, which can delay things by a few days.

If you’re dealing in a sensitive category or don’t have all your business info in order, be prepared for a few extra steps.

What setup looks like:

• Go to your Shopify dashboard
• Navigate to Settings > Payments
• Click Activate Shopify Payments
• Enter required details: legal business name, bank account, personal ID, and tax info (if applicable)

What you’ll need to verify:

• A bank account in a supported country
• A matching name between store owner and account holder
• Personal identification like a passport or driver’s license
• Business registration documents if you’re a corporation or LLC

Getting this info right the first time saves a lot of time. I’ve seen clients lose days waiting for a simple mismatch to be resolved.

What can go wrong:

• If your product category is flagged as high-risk (like CBD, adult, or supplements), Shopify might place a temporary hold on your account
• Stores in unsupported countries won’t even see Shopify Payments as an option and will be forced to use a third-party gateway
• Inconsistent details (for example, your store is under your LLC but the bank is under your personal name) can trigger payout holds or verification issues

Here’s a quick breakdown of common setup scenarios:

As a rule, I tell clients: set it up immediately after launching your store. Don’t wait until your first sale. Submit accurate, verified information, and if Shopify requests additional documentation, respond fast.

Once you’re verified, it runs smoothly. Payouts begin automatically, and you’ll get clear visibility over transactions, chargebacks, and refunds right from the Shopify dashboard.

What I Love About Shopify Payments

After helping hundreds of ecommerce stores over the last decade, there’s a clear pattern with Shopify Payments. It consistently removes friction—both on the admin side and at checkout.

Once it’s activated, it just works. And it works in ways that reduce cost, boost conversion, and streamline your operations behind the scenes.

There’s no need to juggle separate logins for your payment processor, track fees in a spreadsheet, or wait five days for funds to land.

It’s all baked into the Shopify experience, and that simplicity is something many founders underestimate—until they’ve experienced it.

You Save on Fees
Using Shopify Payments eliminates Shopify’s additional third-party transaction fees. If you’re using Stripe or PayPal, Shopify charges up to 2 percent on top of their regular processing rates.

Depending on your plan, here’s what you could be saving per transaction:

That’s real margin back in your pocket, especially once you start processing thousands in monthly revenue.

Payouts Are Predictable
When you’re running ad campaigns or have a team waiting on pay, cash flow matters. Shopify Payments delivers consistent, fast payouts in most regions.

• In the US, UK, and Canada, payouts usually hit your bank within 1–2 business days
• You’ll receive a daily summary of sales and upcoming deposits inside the dashboard
• You can easily track failed payouts or holdbacks, with explanations and next steps provided

This reliability means less time chasing funds and more time running your store.

Supports All Major Payment Methods
Your customers expect to check out in seconds—and with the payment option they already trust. Shopify Payments gives you full coverage across the most popular choices:

• Apple Pay
• Google Pay
• Meta Pay
• Shop Pay (Shopify’s accelerated checkout)
• Standard credit and debit cards (Visa, Mastercard, American Express, Discover)

Offering these reduces cart abandonment and makes your brand feel trustworthy from the very first interaction.

Built-In Fraud and Tax Tools
You also get added peace of mind without needing third-party plugins. Shopify includes a suite of tools that protect both you and your customers:

• Fraud Analysis: Every order includes risk indicators like mismatched billing data, flagged IPs, or unusual order patterns
• Shopify Tax (US only): Calculates sales tax based on your customer’s location and your product type. As of late 2024, it also offers automated filing in select states
• Dispute Management: Pre-filled templates for chargebacks that include order, delivery, and tracking info—making it easier to win disputes

For growing brands, this level of backend control removes a lot of headaches. Instead of piecing together compliance and risk tools, everything lives inside your Shopify account.

And that gives you more confidence to scale.

What Frustrates Me About Shopify Payments

As great as Shopify Payments is, it’s not without its limits. And for some sellers, those limits can be hard blockers.

I’ve worked with brands across all kinds of industries—fashion, digital, wellness, fitness, B2B—and while most benefit from using Shopify Payments, some simply can’t use it due to strict rules around what they sell or where they operate.

The issues don’t usually show up until you’re midway through setup or have already started processing sales.

That’s when the limitations can catch you off guard.

Country Restrictions
Shopify Payments is only available in around 20 countries. These include:

• United States
• United Kingdom
• Canada
• Australia
• Ireland
• Germany
• New Zealand
• Japan
• Singapore
• Spain
• Sweden
• Netherlands

If your business is based outside of these regions, you won’t even see Shopify Payments as an option in your dashboard.

You’ll be forced to use third-party gateways like Stripe, 2Checkout, or PayPal—and you’ll also pay extra Shopify fees for doing so.

Strict Category Rules
Shopify Payments has zero tolerance for what it considers “restricted businesses.” Even if your products are legal, they may still get flagged during onboarding or later down the line.

Here are the most common product types that are not allowed:

• CBD or hemp-derived products (even with proper licensing)
• Adult content, services, or products
• Firearms, knives, or anything classed as a weapon
• Digital subscription services (depends on the format and terms)

These aren’t grey areas. If you fall into one of these categories, Shopify Payments will either block setup or freeze your payouts without warning.

I’ve had clients in the supplement space see their accounts held for weeks while Shopify asked for additional documentation.

No Custom Rates Unless You’re on Shopify Plus

If you want to negotiate lower transaction fees, you’ll need to upgrade to Shopify Plus, which starts at around $2,000/month.

This pricing level isn’t feasible for many businesses unless they’re already pushing well into six figures in monthly revenue.

Everyone else is locked into the flat processing rates based on their plan:

These are competitive, but not negotiable unless you’re on an enterprise-level plan.

Payout Holds
This one frustrates a lot of new store owners. Even after verification, Shopify may hold your first few payouts for up to 30 days, especially if:

• You’ve had chargebacks in the past
• You process a large volume of orders out of nowhere
• You sell products in higher-risk niches

This can cause real cash flow issues, particularly if you’ve already spent money on ads or inventory. The platform doesn’t always give clear timelines, which adds to the stress.

If you’re in a restricted niche or need more flexibility with risk handling and regional support, Stripe or PayPal might still be your best fallback.

They’re not as tightly integrated, and you’ll pay more in fees—but at least you’ll be able to keep the business moving.

Shopify Payments Fees: How It Works by Plan

Understanding Shopify Payments’ fee structure is key if you’re trying to optimise profit margins. The rates are clearly laid out by Shopify plan, and there are no hidden charges or setup fees.

You’ll only ever pay per transaction, which makes this model predictable and easy to build into your cost planning.

Here’s how the fees break down:

Key things to note:

• No setup or platform fees just to use Shopify Payments—it’s included in every plan.
• You only pay per successful transaction. No monthly minimums or usage caps.
• Refunds don’t return transaction fees, which is standard across most processors today.
• If you don’t use Shopify Payments, Shopify adds its own third-party fee on top of what Stripe or PayPal charges you.

This is one of the biggest reasons I recommend activating Shopify Payments unless you’re blocked by location or product category.

That 0.5% to 2% savings per transaction adds up quickly when you’re doing volume.

Shopify Payments vs Stripe vs PayPal

If you’re not sure whether Shopify Payments is the right move, it helps to compare it side by side with the most common alternatives: Stripe and PayPal.

I’ve integrated all three into dozens of stores over the years.

While they each have their place, Shopify Payments stands out when used inside Shopify’s ecosystem.

From a user experience standpoint, Shopify Payments wins when it comes to speed, simplicity, and backend automation—especially for stores doing high-volume sales or working with small teams.

Stripe is more flexible and developer-friendly, which makes it a better fit for headless commerce or marketplaces with custom flows.

PayPal remains widely trusted among consumers, but the redirect flow during checkout can hurt conversions on mobile, which is something to consider if most of your traffic comes from phones.

When I recommend Stripe or PayPal:

• You’re in a country not supported by Shopify Payments.
• You’re selling restricted products like supplements or adult content.
• You want to offer PayPal as a customer preference, which many buyers still trust.

Also worth noting: you can use PayPal alongside Shopify Payments, which gives you more flexibility without sacrificing the benefits of the native processor.

Shopify Checkout + Conversion Boost

Shopify has claimed for years that its checkout is the highest converting in the industry.

After running A/B tests with WooCommerce, BigCommerce, and even headless setups, I can say this claim holds up.

Shopify’s checkout, especially when paired with Shopify Payments, removes friction and creates a faster path to purchase.

Here’s why it performs so well:

• One-Page Checkout
  The latest upgrade gives customers a streamlined view: cart, shipping, and payment details all on one screen. Fewer clicks mean fewer drop-offs.
• Saved Info with Shop Pay
  Customers using Shop Pay can check out in seconds with pre-saved addresses, payment methods, and contact info. It’s especially powerful for mobile shoppers.
• Customizable Checkout Settings
  You can enable options like:
  • Express checkout buttons
  • Local pickup
  • Tipping
  • Delivery instructions
  • Split shipping
• Localized Currency + Language
  Shopify automatically detects the shopper’s browser language and location to show the right currency, tax rate, and language—essential for global stores.

When you combine these conversion features with Shopify Payments’ native integration, it reduces abandoned carts and shortens the path to revenue.

Payouts: What to Expect

Once your Shopify Payments account is verified, payouts begin automatically.

This is one of the areas where Shopify has a clear advantage. There’s no need to manually trigger withdrawals or wait for batch payouts at the end of the week.

Payout times vary depending on your region:

You can view your payout schedule directly inside Admin > Finances > Payouts, along with upcoming deposit dates and completed transactions.

Each payout includes:

• Net revenue after Shopify’s processing fee
• Deductions for refunds, if issued before payout
• Holdbacks for chargebacks, which only apply in flagged or high-risk accounts

If you’ve enabled multi-currency sales, Shopify will automatically convert the currency to your base currency before sending payouts.

Built-In Tools You Get With Shopify Payments

Shopify Payments isn’t just a credit card processor. When you activate it, you unlock a suite of tools that streamline accounting, compliance, and fraud prevention.

Here’s what comes bundled:

• Shopify Tax
  Shopify calculates US sales tax at checkout and, in eligible states, will automatically file and remit tax for you. It keeps you compliant without needing a third-party app like Avalara.
• Chargeback Handling
  If a customer disputes a charge, Shopify generates a pre-filled evidence response. You can review it, edit if needed, and submit it straight from your admin.
• Fraud Analysis
  Every order comes with an automatic fraud score. You’ll see flags like:
  • Mismatched billing vs shipping address
  • Suspicious IP addresses
  • High order velocity from a new customer
• Currency Conversion
  Shopify Payments supports selling in multiple currencies. It displays the price in your customer’s local currency and converts it automatically when the sale is completed.

These features often require separate subscriptions with other processors. With Shopify Payments, they’re included from day one.

Apps That Pair Well With Shopify Payments

To get even more value out of Shopify Payments, I recommend pairing it with purpose-built Shopify apps. These tools help automate operations, drive upsells, and manage risk more effectively.

Top apps to consider:

• ReConvert
  Add post-purchase upsells or thank-you pages right after checkout. Boost average order value without slowing down the buying process.
• Shopify Flow
  Automate actions like tagging high-risk orders or flagging large transactions for review. Ideal for scaling stores with multiple staff.
• AfterShip Protection
  Offers optional insurance at checkout to reduce chargebacks related to shipping issues. Helps build trust and cover your margins.
• Affirm or Klarna
  Add Buy Now, Pay Later options directly into your checkout. These integrate with Shopify Payments and give customers more flexible ways to pay.
• Skio
  If you’re running subscriptions, Skio ties directly into Shopify’s billing engine. It’s much smoother than legacy apps like Recharge.

All of these are available through the Shopify App Store, and most work seamlessly with the Shopify Payments ecosystem.

Shopify Payments Customer Support

Support is another strong point of Shopify Payments—though there are a couple of limitations depending on your plan.

For most payment-related questions, Shopify’s main support team can help, and in my experience, they’ve been responsive and well-trained.

Support channels include:

• Live Chat (24/7):
  Available through the Shopify Help Center. Good for quick fixes or checking on verification delays.
• Phone Support:
  Only available for Shopify Plus customers. Response times are fast and direct when you need priority help.
• AI Assistant (Shopify Sidekick):
  Can now handle simple tasks like checking payout status, locating transactions, or navigating payment settings.
• Dispute Center:
  Located in your admin, this section handles chargeback cases, shows documentation history, and gives you submission deadlines.

The only missing piece? Email support. For more complex billing issues or escalations, having an email thread would help.

But most cases I’ve handled have been resolved via live chat within the same day.

Final Verdict: Should You Use Shopify Payments?

If you’re in a supported country and selling products that meet Shopify’s policy, then yes—use Shopify Payments.

It integrates perfectly with the platform, removes unnecessary fees, and improves the buying experience across every device.

Who it’s great for:

• Ecommerce brands in the US, UK, CA, EU, AU, or NZ
• Product-based businesses with low to moderate risk
• Teams that want to reduce manual reconciliation and admin work

Who should look elsewhere:

• Merchants in unsupported regions like India, South Africa, or most of Latin America
• Brands selling CBD, supplements, or adult products
• Businesses that need advanced custom gateway routing or want to negotiate rates without upgrading to Shopify Plus

I’ve built and scaled hundreds of ecommerce stores, and nine times out of ten, Shopify Payments is what we choose.

It simplifies the financial side of the business and frees up time to focus on what really matters—growth.