Payment Gateway Sync Issues: Stripe, PayPal & Square

Payment gateway synchronization is the most financially sensitive automation in any e-commerce operation. When payment data fails to sync correctly between your gateway and your accounting system, the consequences are immediate: bank reconciliations that do not balance, revenue figures that misstate your financial position, and in the worst cases, customers charged incorrectly. We have debugged payment sync failures across Stripe, PayPal, and Square integrations, and the failure patterns are remarkably consistent across all three platforms.

The Universal Problem: Webhook Reliability

All three major payment gateways rely on webhooks to notify external systems about payment events: charges, refunds, disputes, and payouts. Webhooks are inherently unreliable. They are fire-and-forget HTTP requests that can fail due to network issues, server timeouts, or receiving system downtime. Each gateway handles webhook failures differently, and understanding these differences is critical to building resilient payment sync.

Webhook behavior differs across gateways. Build your automation to handle the weakest guarantees, not the strongest.

Stripe-Specific Sync Issues

Problem: Duplicate payment records in QuickBooks. Stripe webhooks can be delivered more than once. If your automation creates a QuickBooks payment record for every payment_intent.succeeded event without checking for duplicates, you will have inflated revenue figures. The fix is to use Stripe's event.id as an idempotency key. Before creating any record, check whether that event ID has already been processed.

Problem: Payout amounts do not match deposit amounts. Stripe payouts bundle multiple transactions and deduct fees. A payout of $4,847.23 does not correspond to any single order. To reconcile, you need to use the Balance Transactions API to retrieve every transaction included in each payout, then match those against your order records. This is the most common Stripe reconciliation failure we encounter, and the fix requires a dedicated reconciliation workflow that runs after each payout webhook.

Problem: Refund webhooks arrive before charge webhooks. Stripe does not guarantee event ordering. We have observed charge.refunded events arriving before the corresponding charge.succeeded event during high-volume periods. If your automation processes events sequentially, this creates a refund without a matching charge. Implement a queue that checks for dependent events and holds out-of-order events until prerequisites are processed.

PayPal-Specific Sync Issues

Problem: IPN and webhooks running simultaneously. Many businesses have legacy Instant Payment Notifications (IPN) running alongside newer webhook integrations, creating duplicate event processing. PayPal's IPN system and webhook system are independent; they do not deduplicate. If both are active, every transaction generates two notifications. Audit your PayPal account under Developer > Webhooks and Settings > Notifications to identify and disable the redundant system.

Problem: Currency conversion discrepancies. PayPal performs currency conversion at the time of transaction, but the conversion rate is not always included in the webhook payload. When syncing to accounting software, the amount in your settlement currency may differ from what the webhook reports. Always use the seller_receivable_breakdown object to get the actual amount received after PayPal's conversion. For businesses dealing with multiple currencies, see our guide on multi-currency automation challenges.

Square-Specific Sync Issues

Problem: Location-based data isolation. Square's API is organized by location. If your business has multiple locations, payment data from Location A is not automatically visible when querying Location B. Automations built for a single location break when a second location is added because the API returns empty results for the original location-scoped queries. The fix is to implement multi-location awareness: iterate through all active locations and aggregate payment data.

Problem: Tender type confusion. Square transactions can include multiple tenders (payment methods). A single order might have a split payment between a gift card and a credit card. If your automation only syncs the first tender, the recorded payment amount will not match the order total. Parse the full tenders array and create corresponding records for each payment method.

Building Resilient Payment Sync

Regardless of which gateway you use, resilient payment sync requires four architectural components:

• Idempotent processing: Every webhook handler must check whether the event has already been processed before taking action. Use the gateway's native event ID as your deduplication key.
• Polling fallback: Run a scheduled job every 15 minutes that queries the gateway's API for recent transactions and compares them against your records. This catches any webhooks that were lost or failed to process.
• Reconciliation job: Daily, compare the total of all synced transactions against the gateway's settlement report. Any discrepancy triggers an alert for manual investigation.
• Event sequencing: When your automation depends on events arriving in order (charge before refund, authorization before capture), implement a queue that holds events until their dependencies are satisfied.

For businesses using multiple payment gateways, the complexity multiplies. Each gateway has different data structures, different event types, and different timing characteristics. Normalizing this into a unified payment record that your invoice automation and accounting system can consume requires careful architecture. Refer to our article on data mapping errors for the field-level mapping strategies that prevent the most common payment sync failures.

"The goal of payment sync automation is not speed. It is accuracy. A payment record that is synced 5 minutes later but is correct is infinitely more valuable than one synced instantly but wrong."