Shopify Payments & PayPal Express Checkout: Common Issues and Proven Solutions

If you’re running an eCommerce store with Shopify, ensuring smooth, reliable payment processing is crucial to customer trust and your bottom line. At MagentoBrain, we specialize in solving complex payment integration issues—not just for Magento, but for Shopify users as well. This guide tackles two common issues: Shopify Payments payout suspensions and PayPal Express Checkout setup conflicts.

Yes, Shopify Payments and PayPal Express Checkout can be used simultaneously—but they are managed separately.

Shopify Payments is Shopify’s native payment processor, supporting credit cards, Apple Pay, and Google Pay.

This is a fast-track PayPal integration that allows customers to checkout using PayPal directly from the product or cart page.

• PayPal transactions are NOT processed through Shopify Payments.
• Each gateway maintains its own transaction records and payout schedules.
• Shopify automatically creates a PayPal Business account using your store’s email when you sign up. This email must be verified in PayPal to receive payments.

1. Login to your Shopify Admin Panel 
2. Go to Settings > Payments 
3. Under PayPal, click Activate PayPal Express Checkout 
4. Connect your PayPal Business account
5. Confirm the email address in PayPal and ensure it matches your Shopify login

Pro Tip: If you don’t see the PayPal Express button, go to:

• Online Store > Themes > Customize
• Ensure Dynamic Checkout Buttons are enabled

This helps reduce cart abandonment and increases conversions.

One of the most frustrating issues merchants face is “Shopify Payments payouts are pending” or “accrediti in sospeso” (as raised in Italian Shopify forums).

• Identity or document verification incomplete
• Mismatch in personal or banking information
• High-risk activity flagged by Shopify

1. Check the Notifications Tab in Shopify for pending tasks
2. Go to Settings > Payments > Shopify Payments > View Payouts
   
3. If prompted, upload clear documents (e.g. government ID, utility bill, business registration)
4. Contact Shopify Support if verification takes longer than 2–3 business days

Shopify may temporarily hold funds to comply with financial regulations. This is standard and reversible once verification is complete.

MagentoBrain is your go-to partner for all things eCommerce. While Magento is our core expertise, we also provide Shopify development and support, including:

• Shopify payment gateway integration
• PayPal and third-party gateway setup
• Fixing Shopify payout issues
• Custom checkout UX enhancements
• Speed optimization and Shopify SEO

Whether you’re launching a new Shopify store or facing technical roadblocks, our certified developers can resolve them fast.

Shopify Payments and PayPal Express Checkout are powerful tools—but they must be correctly configured to avoid payout holds, missing checkout buttons, and customer payment errors.

Need expert help? Contact MagentoBrain today for Shopify Payments troubleshooting, eCommerce support, and custom Shopify development solutions tailored to your business.