PayMongo is the most popular payment gateway for Philippine online sellers — and for most businesses, the integration with Shopify works well enough out of the box. But "well enough" isn't always the same as "working well."
Merchants across the Philippines encounter PayMongo issues on Shopify on a regular basis: failed GCash transactions, payments confirmed on the customer's end but not reflected in Shopify, escalating costs from hidden platform surcharges, and orders getting flagged by Shopify's fraud system even when nothing is actually wrong.
If you're running a Shopify store and using PayMongo to accept GCash, Maya, and card payments, this blog covers the most common issues — drawn from PayMongo's own troubleshooting documentation and real merchant experiences — along with the practical fixes businesses use to resolve them.
And for merchants who find these PayMongo issues on Shopify keep coming back regardless of what they fix, we'll also look at why some businesses are choosing to move to a platform where many of these problems simply don't exist.
The Most Common PayMongo Issues on Shopify — and How to Fix Them
#1 GCash or E-Wallet Payment Not Reflected in Shopify
This is the most frequently reported PayMongo troubleshooting issue for Philippine online stores: a customer completes a GCash or Maya payment, receives a confirmation on their end, but the order in Shopify stays unpaid or the payment doesn't register.
It happens because GCash, Maya, and other e-wallet payments are processed asynchronously — the customer may close their browser window after paying but before the redirect back to your Shopify confirmation page completes.
Shopify waits for that redirect to confirm the order, but PayMongo's webhook is the actual source of truth for payment status. If your webhook isn't configured correctly, or if Shopify's order processing is delayed, the two systems fall out of sync.
How businesses solve it: Check your PayMongo dashboard first — if the payment shows as 'Paid' there, the money has been received. Then log into your Shopify admin and manually mark the order as paid. To prevent this from happening repeatedly, verify that your PayMongo webhook URL is correctly set in your PayMongo dashboard under Developers > Webhooks, and that it points to your live Shopify store URL (not a test environment). Also confirm you're using live-mode API keys, not test-mode keys, in your Shopify PayMongo plugin settings.
#2 PayMongo Plugin Installed but Not Showing at Checkout
A common setup-related PayMongo issue on Shopify: the PayMongo app is installed from the Shopify App Store, you can see it in your apps list, but GCash, Maya, and card options don't appear on the checkout page.
This usually happens because the plugin was installed but not fully activated as a payment provider — a step that requires a separate action inside Shopify's Settings > Payments panel, separate from the App Store installation itself.
How businesses solve it: Go to your Shopify Admin: Settings → Payments. Scroll to 'Third-party payment providers' or 'Alternative payment methods' and look for PayMongo. If it appears but isn't activated, click 'Activate' and follow the prompts. If it doesn't appear at all, you may need to complete the PayMongo connection flow inside the app itself first. Also confirm that your store currency is set to Philippine Peso (PHP) — the PayMongo Shopify plugin only works for stores with PHP as their currency, and it will not display at checkout if your store is set to USD or any other currency.
#3 Transactions Below ₱100 Are Declined
Philippine Shopify merchants using PayMongo sometimes encounter a specific checkout failure: the customer selects a payment method, proceeds, and the transaction is declined — even when the customer's GCash or card has sufficient balance.
If the cart total is below ₱100, this is expected behavior. PayMongo enforces a minimum transaction amount of ₱100 for all payment methods on the Shopify plugin. Transactions below this threshold will fail regardless of the payment method or the customer's account status.
How businesses solve it: Set a minimum order value in your Shopify store settings to prevent sub-₱100 orders from reaching checkout with a PayMongo payment option. Go to Shopify Admin → Settings → Shipping and delivery → Manage rates, or use Shopify's Script Editor or a minimum order app to enforce the floor. Alternatively, review your product pricing to ensure that even your lowest-priced items, when combined with shipping, exceed ₱100 in cart total.
#4 Shopify Flags PayMongo Orders as High-Risk
Shopify has its own fraud detection system that analyzes every order.
Because PayMongo is a third-party gateway, Shopify doesn't receive all the fraud-screening data it would from Shopify Payments — which means its system has less information to work with and may flag legitimate PayMongo orders as high-risk or suspicious.
This is documented in PayMongo's own Shopify troubleshooting guide and is a structural limitation of how Shopify handles third-party gateway data, not a PayMongo fault specifically.
For Philippine merchants, this can mean manually reviewing orders that are actually perfectly valid, creating unnecessary operational overhead.
How businesses solve it: Don't automatically cancel or refuse orders flagged as high-risk by Shopify when using PayMongo. Instead, cross-reference the order against your PayMongo dashboard — if the payment shows as confirmed in PayMongo, the transaction is genuine. You can also contact PayMongo's support team for guidance on specific suspicious orders by emailing their merchant support. For repeat customers or known buyers, the risk score will typically be lower. Consider installing a dedicated fraud review app that integrates with third-party gateways more effectively than Shopify's native system.
#5 Payment Capture Mode Mismatch Causing Failed Card Transactions
PayMongo on Shopify has two distinct card payment plugins — 'Express Cards via PayMongo' and 'Credit/Debit Card via PayMongo' — and each requires a different payment capture setting in Shopify.
If the wrong capture mode is set, card transactions may appear to succeed on the customer's end but fail to fully process, or orders may sit in a 'Payment pending' state that never resolves. This is a configuration-level PayMongo troubleshooting issue for Philippine online stores that affects card payments specifically.
How businesses solve it: For the 'Express Cards via PayMongo' plugin, go to Shopify Payments settings → Manage under 'Payment capture' → select 'Automatically at checkout.' For the 'Credit/Debit Card via PayMongo' plugin (which uses hold-then-capture), you must select 'Manually capture payment for orders.' Mismatching these settings — for example, running the credit/debit card plugin with automatic capture — is one of the most common configuration errors merchants encounter after switching between PayMongo's card plugin versions.
#6 Double-Fee Structure: Shopify Surcharge on Top of PayMongo
This isn't a technical bug — but it is consistently one of the most painful PayMongo issues on Shopify for Philippine merchants, and it surprises many sellers who didn't fully understand it during setup. Because Shopify Payments is not available in the Philippines, every Philippine Shopify merchant is classified as a third-party gateway user.
Shopify charges an additional platform fee on every transaction processed through PayMongo: 2% on the Basic plan, 1% on the Shopify plan, 0.5% on Advanced. On a GCash payment, this means paying PayMongo's 2.5% plus Shopify's 2% — a total of 4.5% per transaction. On ₱200,000 per month in PayMongo sales, that's ₱4,000 per month — ₱48,000 per year — going to Shopify before a single operational cost is covered.
How businesses solve it: On Shopify, the only way to reduce this surcharge is to upgrade to a higher plan (reducing it to 1% or 0.5%), which may or may not be cost-effective depending on your volume. The deeper fix many Philippine merchants are choosing is switching to a platform that doesn't charge a third-party gateway surcharge at all. Prosperna, built specifically for Philippine MSMEs, integrates PayMongo directly with zero platform transaction fee — you pay only PayMongo's published rates, and not a peso more goes to the platform.
#7 Promotion Discounts Not Reflecting Correctly at PayMongo Checkout
Some Shopify merchants using PayMongo report that promotional discounts — discount codes, automatic discounts, or bundle pricing — don't display correctly in the PayMongo checkout flow, or that the charged amount doesn't match the discounted price the customer expected.
This is a known issue documented in PayMongo's troubleshooting resources and typically relates to how the payment intent is created before versus after discount application.
How businesses solve it: Ensure that all promotions and discount codes are applied before the customer reaches the payment step — promotions added or modified after the payment intent is created may not be reflected. Test your discount flows in PayMongo's test mode before running any promotion campaign. If the issue persists, contact PayMongo's merchant support directly with the specific discount configuration details, as some promotion types require PayMongo-side adjustments to work correctly with the Shopify integration.
#8 Reconciliation Gaps Between Shopify Revenue and PayMongo Settlements
Running PayMongo on Shopify means managing two separate dashboards with two separate reporting systems.
Shopify reports your gross order revenue; PayMongo reports net settlements after fees and refunds are deducted. These numbers never match automatically, and for merchants doing significant daily volume, the weekly reconciliation process — manually cross-referencing Shopify order reports with PayMongo settlement reports — becomes a genuine operational burden.
This isn't a bug but a structural issue that leads to accounting confusion, delayed financial visibility, and errors during BIR reporting periods.
How businesses solve it: Build a simple reconciliation sheet that maps Shopify order IDs against PayMongo payment references on a daily or weekly basis. Use PayMongo's settlement export and Shopify's order export to create a consistent process. Some merchants use third-party bookkeeping apps (such as those that integrate with Xero or QuickBooks) to automate this sync. Alternatively, consider whether a platform with a unified payment and order dashboard — where PayMongo data is visible alongside store data in one place — would eliminate the reconciliation burden entirely.
When Fixing Individual Issues Isn't Enough
For some Philippine merchants, the PayMongo troubleshooting for Philippine online stores listed above is a useful reference to work through one issue at a time.
But for others — particularly those dealing with the double-fee structure, the reconciliation gap, or repeated fraud flags — the pattern of issues points to a structural problem that individual fixes can't fully address.
The root cause isn't PayMongo. PayMongo is a capable, well-built gateway.
The root cause is the friction created by running a Philippine-first payment gateway on a global platform that wasn't designed with Philippine commerce in mind — and that charges Philippine merchants extra for the privilege of using local payment tools.
How Prosperna removes the structural issues
Prosperna is an all-in-one eCommerce platform built specifically for Philippine SMEs.
It integrates with PayMongo directly — giving you access to the same GCash, Maya, card, QR Ph, and online banking coverage — without the platform-level friction that causes most of the issues above:
- Zero platform surcharge on PayMongo transactions — you pay PayMongo's published rates only, eliminating issue #6 entirely
- Unified dashboard — PayMongo payment data visible alongside your orders and inventory, eliminating the reconciliation gap of issue #8
- Built-in Philippine logistics — LBC, J&T, Lalamove, GoGo Xpress, and Grab Express natively integrated, so your payment and fulfillment workflow lives in one place
- Beginner-level payment setup — no cross-platform activation steps, no App Store redirects, no capture mode configuration required
- Local support that understands Philippine payment and commerce context — not a global support queue unfamiliar with PayMongo and BSP regulations
The key insight: Most PayMongo issues on Shopify stem from running a locally-focused Philippine gateway through a global platform not designed for it. Prosperna was built for exactly the opposite: a platform where Philippine payment tools are native, not adapted.
Stop Troubleshooting. Start Selling.
If you're spending hours every month on PayMongo troubleshooting for Philippine online stores — fixing webhook errors, reconciling two dashboards, absorbing Shopify's surcharge, or manually marking paid orders — that's time and money that should be going into your business.
Prosperna gives Philippine sellers a platform where PayMongo integration works the way it should: simple setup, unified reporting, zero platform surcharge, and local support that knows the context.
It's not just a fix for individual issues — it's a foundation where those issues don't arise in the first place.
Try Prosperna free — and accept GCash, Maya, and cards through PayMongo without the Shopify friction.
Frequently Asked Questions
1. Why is my PayMongo payment not showing in Shopify even though the customer paid?
This is usually a webhook or redirect issue. GCash and other e-wallet payments are asynchronous — if the customer closes their browser before the redirect completes, Shopify may not register the payment even though PayMongo has confirmed it. Check your PayMongo dashboard first: if the payment shows as 'Paid' there, the money was received. Then manually mark the order as paid in your Shopify admin, and check that your webhook URL is correctly configured in PayMongo's developer settings.
2. Why is PayMongo not showing at my Shopify checkout?
The most common cause is that the PayMongo app was installed from the Shopify App Store but not activated as a payment provider in Shopify Settings > Payments. The installation and activation are two separate steps. Also verify that your store currency is set to Philippine Peso (PHP) — the PayMongo Shopify plugin only displays at checkout for PHP-currency stores.
3. Does Shopify charge extra when I use PayMongo?
Yes. Because Shopify Payments is not available in the Philippines, Shopify treats PayMongo as a third-party gateway and charges an additional platform fee on every transaction: 2% on the Basic plan, 1% on the Shopify plan, and 0.5% on Advanced. This surcharge applies on top of PayMongo's own processing fees. On Prosperna, there is no additional platform surcharge — you pay only PayMongo's published rates.
4. What is the minimum transaction amount for PayMongo on Shopify?
PayMongo's Shopify plugin requires a minimum cart total of ₱100. Any transaction below this amount will be declined regardless of the customer's available balance or payment method. Set a minimum order value in your Shopify store settings to prevent customers from reaching the PayMongo checkout with a cart below this threshold.
5. Is there a platform that supports PayMongo without Shopify's extra fee?
Yes. Prosperna is a Philippine-built eCommerce platform that integrates PayMongo directly with no additional platform transaction surcharge. You pay only PayMongo's standard published rates per transaction — no Shopify-style platform cut on top. Prosperna also includes native Philippine logistics integrations and a unified dashboard that reduces the reconciliation work that Shopify + PayMongo users typically deal with manually.
Final Thoughts
PayMongo issues on Shopify range from simple configuration mistakes — wrong capture mode, missing activation step, sub-₱100 carts — to structural platform problems that no amount of individual troubleshooting can fully solve: the 2% surcharge on every transaction, the dual-dashboard reconciliation burden, and Shopify's incomplete fraud data for third-party gateways.
The individual fixes above will help you resolve the technical issues. But if you find yourself doing PayMongo troubleshooting for Philippine online stores more often than you're selling, it may be worth asking whether the platform itself is the right fit for a business built on Philippine payment methods and local logistics.
Prosperna was built to answer that question — with a platform where GCash, Maya, and PayMongo work the way Philippine sellers need them to, without the overhead of a global platform catching up to the Philippine market.
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