I’ve used paypal for 14 years, first on another platform, and with shopify for a year and a half. Customers pay either with credit cards or paypal. Credit card payments get deposited into our bank account via shopify payment, and our paypal balance just builds up until I manually transfer to our bank. Usually there are 10-15 paypal purchases a day.
After September 23, we are getting no more deposits into paypal. Has something changed where every payment paid with paypal just comes to us in our regular shopify transfer to our bank?
What could be wrong?
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Shopify doesn’t actually “hold” your PayPal money — it just passes PayPal payments directly into your PayPal account. Normally, nothing Shopify does would move those PayPal funds into your Shopify Payments payouts.
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If PayPal sales have suddenly stopped appearing in your PayPal balance since Sept 23, it usually means one of two things:
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PayPal got disconnected or switched → Shopify may have defaulted those transactions back into Shopify Payments instead of PayPal.
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PayPal account settings changed → Sometimes PayPal updates permissions and requires you to re-authorize the integration in Shopify.
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Customer payment method change → Some buyers who think they’re using PayPal may actually be using PayPal’s credit card option that runs through Shopify Payments, which then deposits to your bank.
What you can check right now:
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Go to Settings > Payments > PayPal in Shopify → make sure it still shows your account connected. If not, reconnect.
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Log into PayPal directly → check if there are any incoming payments after Sept 23.
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Look at a specific order in Shopify that was “paid with PayPal” → see what the payment gateway line says. If it says Shopify Payments instead of PayPal Express Checkout, then PayPal is no longer the gateway.
Likely fix:
Re-connect your PayPal account in Shopify admin. After major platform or API updates, sometimes the PayPal authorization token expires. Re-linking usually restores direct deposits into your PayPal balance.