Introduction
Implementing Shopify PayPal Payments Pro allows you to process credit card payments directly on your checkout page while maintaining the trust associated with the PayPal brand. This integration is particularly useful for merchants who want to offer a professional, on-site credit card experience without redirecting customers to an external site. At HidePay, we help merchants manage how these options appear to ensure the checkout remains clean and high-converting.
This article explains the technical setup of PayPal Payments Pro, how it differs from the standard Express integration, and how to manage the associated fees. We also cover strategic ways to control payment method visibility to protect your margins and reduce cart abandonment. By the end of this guide, you will understand how to leverage this gateway to create a more integrated and efficient checkout experience — or you can install HidePay on the Shopify App Store and begin testing rule-based control in your store today.
Understanding Shopify PayPal Payments Pro and Payflow Pro
For most Shopify merchants, the term "PayPal Payments Pro" refers to the ability to accept credit cards directly on the store while also offering PayPal as an express option. Technically, within the Shopify ecosystem, this is often implemented through the PayPal Payflow Pro gateway.
Unlike the standard PayPal Express Checkout, which redirects the customer to PayPal’s website to complete the transaction, the Pro version allows for transparent credit card processing. The customer enters their card details directly into your Shopify checkout. This reduces friction and can lead to higher conversion rates for shoppers who do not have or do not want to use a PayPal account.
The distinction between these services is important for account configuration. PayPal Express is usually the default for new stores. Moving to the Pro level requires a specific PayPal business account type and manual configuration within your Shopify admin settings.
Setting Up PayPal Payflow Pro on Shopify
If you have decided that an integrated credit card experience is right for your store, you must manually activate the gateway. Note that Shopify generally allows only one primary credit card gateway to be active at a time. If you are currently using Shopify Payments, you would need to deactivate it to use PayPal Payflow Pro as your primary credit card processor.
Follow these steps to configure the integration:
- Access Payment Settings: Log in to your Shopify admin and navigate to the Settings menu, then select Payments.
- Manage Primary Gateway: If you have an active credit card gateway, you must select "Change gateway" or deactivate the current one to make room for the new integration.
- Select the Provider: Under the "Third-party providers" or "Accept Credit Cards" section, search for and select PayPal Payflow Pro.
- Enter Credentials: You will need your PayPal Merchant Login, User ID, Partner ID, and Password. These are generated within your PayPal Manager account, not your standard PayPal consumer login.
- Configure Transaction Mode: Choose whether to "Automatically capture" payments (immediate sale) or "Manually capture" (authorization only). Manual capture is often preferred for stores that need to verify inventory or shipping costs before finalizing the charge.
- Test the Integration: Always perform a test transaction using a different PayPal account or a real credit card to ensure the funds flow correctly into your business account.
Once active, your checkout will show fields for credit card entry alongside the PayPal button. This gives customers the choice to pay via their preferred method without leaving the security of your domain.
Hide, sort, and rename Shopify payment methods using powerful conditions. Customize your checkout and control payment options with HidePay.
Managing Transaction Fees and Costs
Financial management is a critical part of choosing a gateway. PayPal Payments Pro involves a different fee structure than the standard "free" Express Checkout. Most merchants will encounter a monthly service fee from PayPal for the Pro account, in addition to the per-transaction fees.
Standard Transaction Rates
Typical fees for PayPal transactions are 2.9% plus a fixed fee (such as $0.30) per transaction. These rates can vary based on your business location and the volume of sales you process. International transactions often carry a higher fee, sometimes reaching 3.9% or 4.4% depending on currency conversion requirements.
Shopify Third-Party Fees
Because PayPal Payflow Pro is considered a third-party gateway, Shopify may charge an additional transaction fee on every sale if you do not have Shopify Payments active as your primary gateway. These fees typically range from 0.5% to 2% depending on your Shopify plan level. However, if you are a Shopify Plus merchant using Shopify Payments, these third-party fees are often waived for alternative gateways like PayPal.
Strategic Margin Protection
Some merchants find that PayPal's fees for certain regions or specific products eat into their profits. In these cases, it is wise to use a tool to control when the option appears. We built the app to allow merchants to hide payment methods based on specific conditions — see our guide on How to create a payment customization to learn how to target cart totals, countries, or product rules. This ensures you only offer expensive payment methods when it is financially viable for your business.
Using HidePay to Optimize the Checkout Flow
A common challenge with adding PayPal Payments Pro is that it can clutter the checkout page. You might end up with multiple "Express" buttons and standard credit card fields, which can confuse customers. Effective management of these options is essential for a high-converting store — learn how to Sort and Rename payment methods in the Checkout in our help docs.
Our app, HidePay, gives you the ability to sort and rename these methods. For example, if you find that credit card payments through the Pro gateway have lower dispute rates than PayPal Express, you can use the app to move the credit card fields to the top and push the PayPal button further down. Get HidePay for your store to test ordering and naming that emphasize your most profitable options.
You can also rename the payment methods for better clarity. Instead of just "PayPal," you might rename it to "PayPal or Pay Later" to highlight financing options that might encourage higher order values. This level of customization ensures that the most profitable and reliable payment methods are the ones your customers see first.
Rules for Express Checkout Buttons
When you enable PayPal, Shopify often places "Express Checkout" buttons at the top of the payment page or even on the cart page. While these are designed to speed up the process, they can sometimes bypass important steps, such as shipping rate selection or discount code entry.
By using our tool, you can create rules to block these express buttons under specific circumstances — see the help article "Hide the Express Checkout with HidePay" for step-by-step instructions. For instance, if a customer is buying a "Final Sale" item that requires them to tick a mandatory terms-and-conditions box, you can hide the PayPal Express button to force them through the standard checkout flow. This ensures compliance and reduces the likelihood of customer service issues later.
If you need the same rule-based control for shipping options (so shipping rates are selected before payment), consider pairing payment rules with shipping rules using HideShip on the Shopify App Store.
Native Performance with Shopify Functions
Technical reliability is non-negotiable at checkout. Older Shopify apps used "Script Editor" or theme-based workarounds to hide payment methods, which could be slow or prone to breaking during Shopify updates. The modern standard is to use Shopify Functions.
We have built our app on Native Shopify Functions, which means it runs directly on Shopify’s servers. This architecture ensures that there is no delay in the checkout process. When a customer reaches the payment page, the rules you have set—whether hiding PayPal for certain zip codes or sorting credit cards to the top—execute instantly. If you need to build or migrate Functions yourself, consider SupaEasy on the Shopify App Store for codeless function generation and migration.
Global Considerations for PayPal Payments
PayPal is a global leader, but its popularity varies significantly by region. In some European markets, local methods like Klarna or iDEAL are preferred. In parts of Asia, digital wallets dominate.
If you sell internationally with PayPal Payments Pro, consider these geographical strategies and review our guide on how to organize payment methods by country or Shopify Market:
- Regional Relevance: If you ship to a country where PayPal has low adoption, use a rule to hide the PayPal button and promote a local provider instead. This prevents the checkout from looking irrelevant to the local shopper.
- Currency Handling: PayPal handles multiple currencies well, but the conversion fees can be high. If a customer is paying in a currency that is expensive for you to process, you can use our app to show alternative methods that offer better exchange rates for your business.
- Risk Mitigation: Some regions have higher rates of "Friendly Fraud" or chargebacks associated with PayPal. You can set a rule to hide PayPal for specific provinces or countries known for high risk, while keeping it active for your core markets.
Key Takeaways for Merchants
Optimizing your payment stack is not just about adding more options; it is about presenting the right options at the right time.
- Pro vs. Express: Use Payflow Pro if you want an integrated credit card experience; use Express for the fastest setup.
- Credential Management: Ensure you have your PayPal Manager details ready for a smooth manual setup.
- Cost Awareness: Monitor both PayPal’s service fees and Shopify’s third-party transaction fees.
- Rule-Based Control: Use a tool to hide, sort, or rename methods based on cart size, geography, or customer tags to protect your margins.
- Native Stability: Choose apps built on Shopify Functions to ensure your checkout remains fast and secure.
Conclusion
Setting up Shopify PayPal Payments Pro is a strategic move for any merchant looking to professionalize their checkout and provide a more integrated experience. By moving beyond the standard redirect-based checkout, you offer customers a faster, more trustworthy way to pay. However, the added complexity of managing multiple gateways and fees requires a proactive approach.
By using a tool like HidePay, you can maintain full control over your checkout environment. Whether you need to hide PayPal for high-risk orders, sort credit cards to the top for B2B customers, or rename payment options for better clarity, the right rules ensure your checkout is optimized for both conversion and profit. If you’re ready to begin, try HidePay on Shopify and test rule-based customizations in your store.
If you want a combined checkout-and-shipping bundle, learn more in our post Introducing Nextools’ HideSuite: the bundle for smart Shopify merchants, which explains how HidePay and HideShip work together to streamline conversions and cut unnecessary costs.
To start tailoring your checkout experience and protecting your store's margins, install HidePay on the Shopify App Store.
FAQ
Does PayPal Payments Pro remove Shopify's transaction fees?
No, using PayPal as a third-party gateway does not automatically remove Shopify's transaction fees. If you do not have Shopify Payments active as your primary gateway, Shopify may charge an additional fee per transaction (typically 0.5% to 2%). However, if you use Shopify Payments as your primary gateway and PayPal as an additional option, these fees are usually waived for Shopify Plus merchants.
How is PayPal Payflow Pro different from PayPal Express?
PayPal Express redirects the customer to the PayPal website to log in and confirm payment before returning to your store. PayPal Payflow Pro allows the customer to enter their credit card information directly into your Shopify checkout page. This keeps the customer on your site throughout the entire process, providing a more integrated user experience.
Can I hide the PayPal button for specific products?
Yes, using HidePay you can create rules based on the contents of the cart. For step‑by‑step instructions, see the help article "Is it possibile to hide payment methods for certain products?" which explains how to target products and collections when hiding payment options.
Is it possible to rename the PayPal option at checkout?
Yes. Many merchants prefer to rename "PayPal" to something more descriptive like "PayPal / Credit Card" or "PayPal (Pay in 4 available)." Our tool allows you to rename any payment method at checkout to better match your brand's voice or to provide extra clarity to your customers, helping to reduce confusion and cart abandonment. For details on renaming and reordering, see the guide "Sort and Rename payment methods in the Checkout."