Shopify Payments is our top-rated payment processor for Shopify users, delivering a seamless and fully integrated checkout experience for online stores.
In this review, I’ll walk through Shopify Payments’ fees, pros, cons, and how it compares with Stripe and PayPal — so you can decide if it’s the right fit for your store’s checkout and growth strategy.
This includes a thoroughly researched review of Shopify's functionalities where you can find out what makes it one of the best ecommerce platforms. So what if I told you that, with Shopify Payments, you don’t need to hang on to 3rd party gateways anymore?
Shopify Payments Overview
| Shopify Payments | |
|---|---|
| Best For | Stores using Shopify as their ecommerce platform |
| Rating | Excellent – 4.7 out of 5 |
| Recommended For | Growing Shopify stores |
| Sellers in the U.S., UK, AU, and 35+ other supported countries | |
| Avoiding third-party transaction fees | |
| Free Trial | Included with all Shopify plans |
Pros and Cons
Pros
- Integrated into your Shopify dashboard
- Eliminates Shopify’s additional transaction fees
- Supports Apple Pay, Google Pay, and Shop Pay
- Faster payouts than many third-party gateways
- Automatic fraud protection and dispute handling
Cons
- Not available in every country
- Chargeback fees are non-refundable
- Higher fees on international cards
- You lose access if you leave Shopify
- Limited customisation of billing statements
Need a quick summary of Shopify Payments?
I’ve tested it across multiple Shopify stores. Here’s what I’ve found:
What I Like
- It removes Shopify’s additional transaction fees when enabled
- Payouts arrive fast, and the dashboard is easy to manage
- Works seamlessly with Shopify POS and Shop Pay
- Requires no third-party account to start accepting payments
- Makes reconciling payments and orders simple for accounting
What I Don’t Like
- You’re fully locked in — you lose all access if you switch platforms
- Not available in all countries, so some sellers are excluded
- $15 chargeback fees apply regardless of outcome
- International processing fees can add up quickly
- You can’t always customise what appears on customer billing statements
Shopify Payments used to be available in only a handful of countries, which meant many store owners had to rely on third-party gateways and pay extra transaction fees.
That’s no longer the case. As of 2025, Shopify has significantly expanded its payment support, now offering Shopify Payments in over 35 countries including major markets like Germany, France, Italy, Japan, Mexico, and Singapore.
This wider availability gives more merchants access to lower fees, faster payouts, and a fully integrated checkout — without needing to patch together external processors.
My Experience Using Shopify Payments
Setting up Shopify Payments was simple and took less than 10 minutes to complete. It’s built into the Shopify dashboard, so no external integration or third-party account was required to start accepting payments.
After entering some basic business information — such as company name, EIN (or SSN), and bank details — Shopify Payments was enabled and ready to go. There were no additional approvals needed, unless the store was flagged for risk, which I’ll explain further below.
What You’ll Need to Get Started:
- Your business entity name (LLC, sole proprietorship, etc.)
- Federal tax identification (EIN for businesses or SSN for individuals in the U.S.)
- A checking account in your business name
- Physical business address and contact details
Once the setup was complete, I was immediately taken to the Shopify Payments dashboard, which integrates cleanly with the Shopify admin area. From here, I could view transaction history, payout schedules, processing fees, refunds, and chargebacks all in one place.
Dashboard Insights and Payout Management
The Shopify Payments dashboard stood out for its clarity. All key payment activity was visible at a glance, and payout breakdowns were easy to track.
Highlights from the dashboard:
- Total payouts and fees are grouped by date and payout batch
- Refunds and disputes show status in real time
- Sales tax reports and processing fees are clearly itemized
- Exportable reports help with reconciliation and bookkeeping
Compared to third-party processors like Stripe or PayPal, Shopify Payments offers similar reporting functionality, but with the added benefit of being built directly into the ecommerce platform. That means fewer logins, fewer tools, and fewer errors.
Payouts arrived in two business days after the transaction, which is consistent with industry standards. Timing was reliable across U.S., UK, and Australian accounts.
Refunds, Chargebacks, and Risk Holds
Refunds are processed immediately within the Shopify admin. The amount is deducted from upcoming payouts. If there’s not enough in the balance, Shopify debits the connected bank account. This mirrors how Stripe and other major processors operate.
Chargebacks were straightforward to manage — Shopify pre-fills most of the required dispute response with order and customer data, which simplifies the process.
Key considerations:
- Refunds are deducted automatically from future payouts
- Chargeback fee: $15 per dispute (non-refundable, even if you win)
- Shopify provides dispute evidence templates preloaded with customer data
- You cannot block chargebacks, only respond to them
One point worth flagging — if your store has a sudden increase in volume, high refund rates, or lists restricted items (like digital products), your payouts may be placed on hold for manual review.
This isn’t unique to Shopify Payments — all processors have fraud detection measures — but the transparency and response time from Shopify support could be improved in these situations.
Shopify Payments Fees (Here’s What You Actually Pay)
Shopify’s fees depend on your plan, payment method, and whether you’re using Shopify Payments or not.
On the surface, Shopify's pricing looks straightforward — but once you start scaling, every 0.1% fee makes a real difference to your bottom line.
If you’re using Shopify Payments, you avoid the platform’s additional transaction fees.
But if you use a third-party gateway like Stripe or Authorize.net, Shopify will still take a cut — and that cut varies by plan.
Credit Card Fees by Plan (U.S.)
This table breaks down the card processing rates for online and in-person transactions:
| Plan | Online Rate | In-Person Rate | Additional Fees (if using third-party gateway) |
|---|---|---|---|
| Basic | 2.9% + 30¢ | 2.6% + 10¢ | 2% |
| Grow | 2.7% + 30¢ | 2.5% + 10¢ | 1% |
| Advanced | 2.5% + 30¢ | 2.4% + 10¢ | 0.5% |
These rates apply only if you’re using Shopify Payments. If you opt for another gateway, the listed transaction fee (2%, 1%, or 0.5%) is added on top of the payment provider’s fee.
So if Stripe charges 2.9% + 30¢ and you’re on the Basic plan without Shopify Payments, your total fee per transaction would be 4.9% + 30¢.
I’ve seen this mistake often — store owners think they’re saving time by using PayPal or Stripe as their default, but end up paying hundreds or even thousands more in fees per month without realizing it.
Other Hidden Fees to Watch Out For
While Shopify’s listed rates are predictable, there are a few extra charges that can quietly eat into your margins if you’re not careful:
- Currency conversion: If your store currency differs from the card’s currency, Shopify adds a 1% conversion fee. This is common if you sell globally but price in USD.
- American Express cards: Processed at the same rate as Visa and Mastercard, but Amex tends to have higher dispute rates and lower acceptance internationally.
- Chargeback fees: Shopify charges $15 per dispute, non-refundable. This is consistent across plans and applies whether you win or lose the case.
If you sell digital products, high-ticket items, or operate in industries with above-average refund risk, budget for chargebacks as part of your cost of doing business.
Monthly Plan Costs
Choosing the right plan impacts your transaction fees — and the higher the order volume, the more important this decision becomes.
| Plan | Monthly Price (Annual Billing) | Monthly Price (Month-to-Month) |
|---|---|---|
| Basic | $29 | $39 |
| Grow | $79 | $105 |
| Advanced | $299 | $399 |
If you're doing under $5K/month in revenue, the Basic plan offers enough functionality to get going. But once you’re processing $10K/month or more, it may be worth moving up to the Grow or Advanced plan purely for the savings on transaction fees.
Let’s break it down with an example:
- $10,000/month in online sales
- Average transaction size: $100
- Number of transactions: 100
On the Basic plan:
100 orders × (2.9% + 30¢) = $320 in fees
On the Shopify plan:
100 orders × (2.7% + 30¢) = $300 in fees
That $20 difference might not seem huge, but if you’re scaling past $50K/month, upgrading your plan becomes a cost-saving strategy rather than an expense.
Key Takeaway
If you’re not using Shopify Payments, you’re leaving money on the table.
But even if you are, the plan you’re on directly impacts your processing fees. Once your store gains traction, do the math — those 0.2% differences stack up quickly, especially with repeat customers and high AOV.
Also, keep an eye on those “invisible” fees like chargebacks and currency conversions. They’re easy to overlook but can quietly eat 1–2% of your total revenue if you’re not tracking them regularly.
Shopify Payments vs Stripe vs PayPal
I’ve tested all three processors across Shopify stores to see how they compare on key factors like ease of use, buyer trust, and payout speed.
While Shopify Payments is the most streamlined choice for Shopify users, Stripe and PayPal still have strong advantages depending on the type of store you’re running.
Below is a side-by-side comparison based on core features:
Feature Comparison Table
| Feature | Shopify Payments | Stripe | PayPal |
|---|---|---|---|
| Integrated with Shopify | Yes | No | Yes |
| Payout speed | 2–3 business days | 2–3 business days | Instant to 1 day |
| Buyer trust | Low | Medium | High |
| Chargeback fee | $15 | $15 | $20 |
| Global availability | Limited (21 countries) | Broad (100+ countries) | Broad (200+ countries) |
| Accepted payment methods | Credit/debit, Apple Pay, Shop Pay | Credit/debit, Apple Pay | PayPal, Venmo, credit/debit |
When Shopify Payments Is the Best Fit
Shopify Payments is a strong option for businesses using Shopify exclusively and looking to simplify their payment setup.
Best use cases:
- You’re using Shopify as your ecommerce platform
- You want to avoid additional transaction fees (up to 2%)
- You don’t need advanced billing tools like subscriptions or metered usage
The checkout is streamlined and fully integrated. Shopify handles disputes, refunds, and payout management natively — reducing reliance on external tools.
Where Stripe or PayPal Might Be a Better Option
There are scenarios where Shopify Payments either doesn’t work or doesn’t go far enough.
Consider Stripe or PayPal if:
- You need subscription billing or metered usage (Stripe excels here with its API and flexibility)
- Your store operates in a country not supported by Shopify Payments (e.g., India, Philippines, Pakistan)
- You’re selling digital products, services, or high-ticket items, where buyer trust is key
- You want to offer PayPal and Venmo, which many customers still prefer, especially in the U.S. and Europe
Stripe is the most developer-friendly option and allows for more customization in checkout flows, billing logic, and fraud prevention. PayPal offers instant brand recognition, which can reduce cart abandonment — particularly for new or unknown brands.
Recommended Setups Based on Store Type
| Store Type | Recommended Setup |
|---|---|
| Shopify store in U.S./UK/AU | Shopify Payments (primary) + PayPal (backup) |
| Subscription-based business | Shopify Payments + Stripe + subscription app |
| International or unsupported region | Stripe or 2Checkout + PayPal |
| High-ticket or trust-sensitive products | Shopify Payments + PayPal |
What Shopify Doesn’t Tell You About Shopify Payments
Shopify Payments is marketed as an all-in-one solution for payment processing, and for many stores, it does the job well. But after hands-on testing and reviewing how it works across different use cases, I uncovered several drawbacks and limitations that aren’t made clear upfront.
These issues don’t affect every merchant — but they’re worth knowing before you commit.
Lock-In Effect
Shopify Payments is only available to Shopify users. If you leave Shopify, you lose access to the entire system.
- Your store’s payment processing setup cannot be transferred to another platform.
- All saved customer payment data stays within Shopify — you’ll need to ask customers to re-enter card details elsewhere.
- This is particularly problematic for subscription stores or businesses with high customer retention.
- You’ll also lose Shopify's built-in checkout optimizations, like Shop Pay, once you leave the platform.
This makes Shopify Payments a high-convenience, low-portability solution. It’s ideal for long-term Shopify users, but less flexible for multi-platform sellers.
Risk Flags and Account Holds
Shopify Payments is powered by Stripe in the backend, and like all processors, it uses automated fraud detection systems. The result? Some accounts may experience delayed payouts or reviews — even if nothing is technically wrong.
During testing, I noted several scenarios that triggered account holds:
- Sudden spikes in daily sales
- High refund rates or chargebacks
- Selling digital goods, services, or “high-risk” products (e.g. CBD, supplements)
- Incomplete business information or lack of policies on the website
When flagged, payouts may be paused for up to 5–7 business days while Shopify manually reviews the account. Merchants are usually notified, but the lack of real-time updates from support can make this frustrating.
To reduce your risk of payout holds:
- Upload clear return, shipping, and privacy policies
- Avoid selling prohibited items without approval
- Use your real business name and provide contact info on your store
Refunds Are Pulled From Future Payouts
Shopify Payments processes refunds instantly, but they deduct the amount from your next payout. If your payout balance is too low, Shopify will debit your linked bank account.
What this means for sellers:
- Issuing multiple refunds in a short time can lead to cash flow issues, especially for newer stores.
- There’s no built-in refund buffer or warning system — the funds are simply removed.
- If a refund is issued after a payout has already been sent, it will come directly out of your bank account.
This system is common among processors, but new merchants often don’t realise it. It's important to monitor your balance and factor refund volume into your cash flow planning.
Limited Customization of Billing Descriptors
The billing descriptor is what appears on your customer’s credit card statement. With Shopify Payments, this defaults to either “Shopify” or a simplified version of your store name.
- If your store’s domain or brand name doesn’t match the billing descriptor, it can lead to confusion or disputes.
- Customers who don’t recognize the charge may file a chargeback, even if the order was legitimate.
- To change the descriptor, you’ll need to submit a support request — and changes aren’t always approved.
Stripe and PayPal allow more customization by default. If brand consistency on customer statements is a priority for you, this is something to be aware of.
Is Shopify Payments Right for Your Business?
Shopify Payments is a powerful option for Shopify users — but it’s not for everyone. Whether or not it’s the right fit depends on your store’s size, revenue, location, and level of technical complexity.
Below, I’ve broken down who it suits best and when it might fall short, based on real-world testing and the most common scenarios I’ve seen across ecommerce stores.
New Sellers (Under $5K/month)
If you’re just starting out, Shopify Payments is the easiest and most cost-effective choice.
Why it works:
- No need for third-party integrations or setup
- You’ll avoid Shopify’s 2% transaction fee (applied if you don’t use Shopify Payments)
- Works straight out of the box — all settings are pre-configured
- Ideal for physical product sellers in supported countries like the U.S., UK, Canada, and 35+ other supported countries
The only caution here is for digital or service-based sellers. These product types are more likely to trigger risk flags or manual reviews.
Growing Brands ($5K–$100K/month)
At this stage, Shopify Payments is still a great option — but optimization starts to matter.
What to consider:
- Upgrade to the Shopify or Advanced plan to lower card processing fees
- Add PayPal as a secondary option to capture buyers who prefer branded checkout
- Monitor refund volume and chargebacks more closely, as they impact payout reliability
- If selling globally, factor in the 1% currency conversion fee on international cards
For most mid-level brands, Shopify Payments continues to be the best fit thanks to its convenience and reduced fees when compared to external processors.
High-Volume Sellers ($100K+/month)
At enterprise level, Shopify Payments remains viable — but many brands start building out more complex setups.
What advanced stores typically do:
- Negotiate custom rates with Shopify directly (available at high volumes or through Shopify Plus)
- Add Stripe or Braintree for subscriptions, invoicing, or recurring billing
- Use third-party tools to manage fraud protection, chargebacks, and tax automation
- Maintain multiple gateways to reduce risk if one provider places a hold or delay
Shopify Payments holds up well in performance and integration. But at this scale, most businesses build a hybrid stack to improve redundancy and control.
International Sellers
Shopify Payments is not available in every country. If your business is based in an unsupported region, you’ll be required to use a third-party gateway.
What to expect:
- Shopify adds an additional 0.5% to 2% fee per transaction when using external processors
- You’ll also pay the regular Stripe, PayPal, or 2Checkout fees
- This combined fee can exceed 5% per sale, depending on your plan and volume
- Customer payment methods may be limited depending on the region
In these cases, Shopify Payments isn’t an option — but it’s still important to weigh the platform fees when selecting a gateway.
Final Verdict: Is Shopify Payments Worth It?
Shopify Payments is the best payment solution for most Shopify users. It’s fast to set up, fully integrated into your store, and removes Shopify’s additional transaction fees — which can save merchants up to 2% per order. It performs well across all key areas like payout speed, dashboard clarity, and overall ease of use.
For sellers who are using Shopify exclusively and operating in a supported country, it’s the most seamless option. You’ll benefit from an all-in-one ecosystem where everything — orders, payments, payouts, and refunds — is managed from one place.
When I Recommend Shopify Payments
Based on my experience, I’d recommend Shopify Payments if:
- You’re selling in the U.S., UK, Canada, or Australia
- You want to reduce third-party complexity and cut out extra fees
- You don’t need custom checkout logic or subscription billing
- You’re focused on physical product sales, not digital or high-risk items
It’s especially useful for growing brands, thanks to lower fees on higher-tier plans and faster reconciliation for accounting teams.
When It Might Not Be the Best Fit
Shopify Payments won’t work for every business model. Here’s when I’d suggest looking at Stripe or PayPal instead:
- Your store is based in a country not supported by Shopify Payments
- You need advanced billing features like metered subscriptions or invoicing
- You’re in a high-risk category (digital products, health products, adult, or supplements)
- You want more control over branding and checkout customization
Also, if you want to build a multi-platform business or expect to leave Shopify in the future, relying solely on Shopify Payments can create issues with data portability and subscription continuity.
My Recommended Setup
For most stores I’ve reviewed or tested, the ideal combination is:
- Shopify Payments as the default processor
- PayPal enabled as a secondary checkout option
- Stripe integrated separately for high-volume or subscription orders, if needed
This gives you the best of all worlds: low fees, buyer trust, and redundancy in case of account holds or technical issues.
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