Troubleshooting Subscription Payment Issues After Changing Payment Gateways
If you're having an issue with subscription billing going through after switching payment gateways on your Shopify store, check out this guide
Written by Adriana Giancarla
Updated Nov 5, 2026 3 min read
If you've recently changed your payment gateway on Shopify and noticed that your subscription transactions are not going through, this guide will help you understand the situation and take appropriate steps to resolve it. Please note that Ongoing acts as a facilitator in subscription management, and we do not handle the actual approval or denial of transactions.
Are you currently seeing the message "merchant is not accepting payments at this time" on checkout for subscription products only, then this article is also for you.
How Ongoing Works
Ongoing is a subscription management app that:
Informs Shopify and your payment gateway that a subscription order needs to be processed.
Stores the results of the transaction (approved or denied) for you to manage your subscription orders.
Facilitates retries for failed transactions by notifying Shopify/the payment gateway to attempt the transaction again.
Important: The approval or denial of transactions is handled entirely by Shopify and the payment gateway you’ve selected. Ongoing is not involved in the actual transaction processing.
Common Reasons for Subscription Payment Failures
New Payment Gateway Approval Delays:
Some payment gateways take time to approve recurring transactions when they’re newly activated. It may take a couple of days for subscription payments to be processed successfully.
Unsupported Payment Gateway for Subscriptions:
Ensure your payment gateway is approved for subscription transactions. Shopify supports subscription payments through:
Shopify Payments
PayPal Express
Stripe
Authorize.net
If your gateway is not one of these, it may not support recurring payments.
Customer Payment Method Incompatibility:
If your previous gateway supported PayPal and you switched to a gateway that doesn’t, any customers using PayPal as their payment method may experience failed transactions.
Industry Restrictions:
Some payment gateways have restrictions on specific industries, such as pharmaceuticals or supplements, and may decline subscription payments for these types of products.
Customer-Specific Issues:
There could be issues with individual customer payment methods, such as being tied to PayPal solely, and not having a regular credit card on file.
Steps to Resolve the Issue
Reach Out to Shopify Support
Contact Shopify Support to confirm that your payment gateway is approved for subscription transactions. ( Shopify > Settings > Payments )
2. Switch to an Approved Payment Gateway
Choose one of Shopify’s supported payment gateways listed above. Once this is set up, Shopify will start processing your subscription transactions successfully.
3. Verify Your Payment Gateway Compatibility
Double-check that your gateway supports the payment methods your customers use
Example: If customers use PayPal as their payment method, PayPal will need to be reactivated to process PayPal payment methods on file)
4. Contact Ongoing to Retry Billing
After you’ve selected and configured a supported payment gateway, reach out to us! We’re happy to manually retry all billing with the new setup and help reactivate any subscriptions that were previously declined.
If subscriptions have a "Declined" status they will need to be reactivated in order to restart the automatic billing again.
When to Contact Support
Shopify Support:
If you suspect an issue with your payment gateway configuration.
To verify compatibility with subscription payments.
Payment Gateway Support:
If transactions are being denied without a clear reason.
To resolve specific issues with recurring payment processing.
Ongoing Support:
If you need help facilitating retry attempts for failed transactions.
For guidance on managing subscription orders in the app.
By following these steps and clarifying the roles of Shopify, your payment gateway, and Ongoing, you can quickly identify and resolve subscription payment issues. If you have further questions, don’t hesitate to reach out to our support team for assistance.
Related Article:
Resolving Subscription Failures Due to an Unapproved Payment Gateway
Related keywords:
payment processor
paypal
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payment gateway
declined billing
switched payment gateways
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merchant is not accepting payments at this time
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