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When choosing a payments processor, businesses have a lot of goals in mind. In addition to keeping fees low, you want to make sure the service is reliable, fast, and able to offer your customers a smooth experience. So, when it comes to comparing platforms, major players like Stripe and Shopify Payments are likely to top your list.
When choosing a payment processor, businesses have a lot of goals in mind. In addition to keeping fees low, you want to make sure the service is reliable, fast, and able to offer your customers a smooth experience.
So, when it comes to comparing platforms, major players like Stripe and Shopify Payments are likely to top your list. Both of these platforms are excellent, particularly for budding startups, but are they the right fit if you want to scale up fast?
While they may not offer the same in-depth reporting and analytics as an advanced platform, such as Baremetrics, a side-by-side comparison will help you make an informed decision.
Stripe Overview & Features
Stripe is a payment service provider rather than a merchant account provider. Knowing the difference between these two types of providers is the first step in figuring out what your business needs.
A payment service provider like Stripe is a third-party that will take payments on behalf of your business, charging transaction and processing fees accordingly, and then later transfer the money into your bank accounts.
What’s interesting about Stripe is that they’ve tried to become an all-in-one platform for business payments. They have over 450 integration options and offer services like a terminal for in-person payments, business financing, and more.
Key Features of Stripe
- Accept Apple Pay and Google Pay
- Accept all major credit cards and debit cards
- Accept local and international payments
- Accept ACH debit and wire transfers
- PoS (Point of Sale) system available
- Accept over 135 currencies
- Available in 36 countries
- Average payout time of 2 business days
- 24/7 support via chat, phone, or email
All in all, Stripe is ideal for businesses who want an easy-to-setup payment processing tool they can have running quickly.
As a flexible solution, Stripe is a great starting point for businesses that don’t use Shopify to handle their eCommerce business.
Check out: Stripe Reports: What Is and Isn’t Available
Shopify Payments Overview & Features
Shopify Payments is actually a payment gateway that runs on Stripe, which is why you’ll see so many similarities between the two options.
In reality, the only reason a business will choose Shopify Payments is if they’re already using Shopify to process their eCommerce sales in a seamless checkout experience. Shopify Payments also offers just about the same payment options as Stripe.
If you’re just starting out, choosing Shopify Payments will allow you to bundle a payments processor (i.e., Stripe) with an eCommerce platform (i.e., Shopify) so that you don’t have to worry about hiring developers or designing your storefront.
Key Features of Shopify Payments
- Accept Apple Pay and Google Pay
- Accept all major credit cards and debit cards
- Accept local and international payments
- Accept over 85 currencies
- Available in 15 countries
- Average payout time of 2 business days
- 24/7 support via chat or phone
If you’re already using a Shopify plan, Shopify Payments is a simple, streamlined way to process payments in your Shopify store.
Related: Shopify Markets: What Shopify Partners Need to Know
Pricing & Transaction Fees
Since Shopify Payments runs on Stripe, both have very similar fee structures and accept practically the same payment methods.
The only real difference is that Shopify Payments requires you to factor in your Shopify membership, which is the only type of monthly fee you’ll have to pay to use the service.
Stripe Fees
- 2.9% and $0.30 per online payment
- 2.7% and $0.05 per in-person payment
- In-person transactions require you to purchase a card reader, which Stripe sells for $59 or $299
See Also: Stripe vs Gumroad: Features, Pricing, Reviews, and More
Shopify Payments Fees
- Shopify monthly membership required, which starts at $29/month
- 2.9% and $0.30 per online payment
- 2.7% and $0.05 per in-person payment
- In-person transactions require you to purchase a card reader, which Stripe sells for $59 or $299
Implementation
Another factor to consider as you compare and contrast Shopify vs. Stripe is the implementation process.
Stripe Implementation Process
The complexity of the Stripe implementation process depends on your company’s needs. While some startups can simply integrate Stripe for payment processing on their website, other companies may need to use the API to build custom integrations.
For example, according to Stripe, implementing Stripe Payments can take anywhere from a week to three months. Luckily, Stripe offers in-depth implementation guides for all of their services that you can use as support.
Shopify Payments Implementation Process
If you’re already using Shopify as your online storefront, implementing Shopify Payments is seamless. However, if you’re not using Shopify, you’ll need to migrate before using Shopify Payments, which can be a complex task if you’re already established.
Stripe vs. Shopify Payments: Pros & Cons Overview
Just like any other platform, both Stripe and Shopify Payments have their pros and cons. Here’s a quick overview of those advantages and disadvantages.
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Related Read: Stripe Analytics Alternative
Which Platform is Best for Your Business?
Both of these solutions make the checkout process simple to set up and manage, with the ability to easily accept credit card payments and a variety of other options that will be sent straight to your Stripe account.
They also offer a PCI-compliant payment process along with a high-risk detection functionality that will help prevent chargebacks — all of which make them powerful business tools.
Stripe offers an easy-to-setup solution for small businesses, and Shopify Payments allows new store owners to bundle that easy payment solution with a point-and-click online store.
Of course, there comes a time when a business outgrows the offerings of Stripe and similar providers, and that’s why Baremetrics exists.
See Also: Shopify Marketplace Kit: What it is and How to Use it
Power Your Growing Business With Baremetrics
Are you considering launching an online store? Do you already run a successful eCommerce business? If you’ve determined that Stripe or Shopify Payments can’t offer the features you need, or if your plans to scale don’t quite fit into the restrictions of these service providers, we encourage you to learn more about Baremetrics.
With in-depth reporting and analytics, Baremetrics will help you gain more insights into your customers through segmentation, forecasting, and benchmarks that will help you thrive.
Frequently Asked Questions
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What is the difference between Stripe and Shopify Payments for subscription businesses?
Stripe is a standalone payment processor that works across any platform, while Shopify Payments is a Stripe-powered gateway built exclusively for Shopify stores.
For SaaS founders and subscription businesses, this distinction matters. Stripe gives you flexibility: 450+ integrations, API access for custom billing logic, and support in 36 countries across 135 currencies. Shopify Payments bundles payment processing with an eCommerce storefront, but it is only available if you are already on a Shopify plan. If you are running a B2B subscription product, Stripe is almost always the better fit since Shopify Payments is designed around one-time eCommerce checkouts, not recurring revenue models. -
Which is cheaper: Stripe or Shopify Payments for handling recurring subscriptions?
Transaction fees are identical at 2.9% plus $0.30 per online payment, but Shopify Payments requires a monthly Shopify membership starting at $29 per month, making Stripe cheaper for most subscription businesses.
For a SaaS company processing recurring billing, that monthly platform fee adds up over time without providing meaningful subscription management features in return. Stripe has no monthly fee and integrates directly with subscription analytics tools. Once you are tracking MRR, churn, and LTV seriously, you will also want a dedicated analytics layer on top of your payment processor. Baremetrics connects directly to Stripe to surface those metrics in real time, with no manual calculations needed. -
What platforms offer automated failed payment recovery for subscription businesses?
Baremetrics Recover is a purpose-built tool that automatically retries failed payments on a smart schedule to reduce involuntary churn for subscription businesses using Stripe.
Failed payments are one of the most common causes of involuntary churn, and most payment processors including Stripe do not handle retry logic intelligently on their own. Recover sends automated card update emails, in-app prompts, and retries payments at optimal intervals to win back revenue that would otherwise be lost. For subscription businesses with $10K or more in MRR, even a small reduction in failed payment churn can meaningfully improve net revenue retention. You can learn more at baremetrics.com/recover. -
How do I measure and reduce involuntary churn caused by failed payments?
Involuntary churn from failed payments is measured by tracking how many cancellations stem from billing failures rather than customer decisions, and reduced by automating payment retries and proactive card update outreach.
Many SaaS teams do not track this separately, which means they misread their churn rate and miss an easy recovery lever. The first step is splitting your churned MRR into voluntary and involuntary buckets. Baremetrics surfaces this breakdown automatically from your Stripe data, so you can see exactly how much revenue is lost to failed payments each month. From there, the Recover feature retries failed charges and contacts subscribers before their access lapses, reducing involuntary churn without any manual work from your team. -
How can I benchmark my SaaS churn rate against similar subscription companies?
You can benchmark your churn rate against comparable SaaS companies using Baremetrics Open Benchmarks, which aggregates real MRR, churn, and LTV data from hundreds of subscription businesses.
Knowing your raw churn number is useful, but knowing whether it is high or low for your stage and pricing tier is what drives action. Baremetrics publishes benchmark data broken down by revenue range, so you can compare your monthly churn rate and net revenue retention against businesses at a similar scale. This is especially useful for SaaS founders preparing investor reports or trying to prioritise whether to focus on acquisition or retention. Generic industry averages are too broad to be actionable; cohort-level benchmarks from real subscription data are not.