Your Shopify Integration Can Stop Silently. How to Check It

If your Shopify store sends orders to an ERP, a warehouse system or an accounting tool through a custom app, that connection can stop working without anything on the store looking wrong. Orders keep coming in. They just stop arriving on the other side. On 25 September 2026 Shopify added logs and health metrics for custom apps to its Developer Dashboard, which makes this far easier to catch. Here is how integrations fail quietly, what the new dashboard shows, and what to ask your developer.

Everything below is from Shopify's changelog and developer documentation, checked on 28 September 2026.

How does a Shopify integration fail without anyone noticing?

Most integrations hear about new orders, stock changes and refunds through webhooks: Shopify sends a message to your app's server every time something happens. If that server does not answer, Shopify tries again, but not forever.

According to Shopify's webhook troubleshooting documentation, your app "must respond to the webhook within five seconds," and Shopify "retries failed webhook calls up to eight times in a four-hour period." After that, "if failures persist, the subscription is removed."

Read that sequence from a merchant's side. Your integration's server goes down on a Saturday night, or a deployment breaks it, or a hosting bill goes unpaid. Four hours later Shopify stops sending it anything. When the server comes back, nothing arrives, because the subscription it depended on is gone. The store takes orders normally, the admin shows nothing unusual, and the warehouse simply receives fewer orders than it should until someone notices the gap.

What are the signs your integration has stopped?

They show up in operations, not in Shopify:

• Orders in Shopify that never reached the warehouse or ERP, usually discovered when a customer asks where their parcel is.
• Stock levels drifting between Shopify and the system that is supposed to be the source of truth, leading to overselling or items shown as sold out that are on the shelf.
• Invoices or accounting entries missing for a block of days.
• A gap that starts at a specific time and continues, rather than random missing records. That pattern points to a subscription that stopped, not to occasional errors.

If any of these sound familiar, the new dashboard is the fastest way to confirm what happened. We cover the wider set of problems in what breaks in a Shopify ERP integration.

What did Shopify add to the Developer Dashboard?

A monitoring view for apps, including custom apps. The 25 September changelog entry describes "API request volume, error rates, webhook delivery health, and embedded admin page load speed," a filterable stream of every API request, webhook delivery and app event, and a home page showing what needs attention across all apps.

The monitoring documentation fills in the detail:

• Logs record "Admin API requests, webhook deliveries, Function runs, UI extension errors, and your own app events" in time order.
• Logs are "retained for 30 days," and a single query can span up to 7 days. You can filter by time, event type, shop and status code.
• A webhook failures alert fires when deliveries are failing often enough to put subscriptions at risk. The documented threshold is "more than 0.5% of deliveries failing across at least 500 deliveries in 24 hours."

Who can see these logs?

Whoever has app development access in the Dev Dashboard. Shopify's Dev Dashboard documentation notes that the monitoring home "requires app development access," and a role that covers stores but not apps opens on the stores view instead.

In practice that usually means your developer or agency, not you. That is fine, as long as someone is actually looking. The risk is a custom app built once, handed over, and never monitored by anyone, which is common when the original developer has moved on.

Custom apps are now created and managed in the Dev Dashboard, and Shopify's help pages say apps created in the admin before 1 January 2026 are managed there as legacy apps. The monitoring documentation does not say whether those legacy apps get the same logs, so if your integration is older, ask your developer to confirm where its monitoring lives.

What should you ask your developer?

Five questions, and the answers tell you quickly whether the integration is being looked after:

1. Who receives the webhook failures alert? If the answer is nobody, or an inbox nobody reads, that is the first fix.
2. What happens if the subscription is removed? A well built app checks its own subscriptions and re-registers them. Shopify's documentation says that after downtime you should recover "by re-subscribing to your webhook topics (if applicable) and importing the missing data."
3. Is there a reconciliation job? Webhooks are not meant to be the only record. A scheduled check that compares recent orders in Shopify against orders in the ERP catches anything that slipped through, whatever the cause.
4. How fast does the app answer? The five second limit means an app that does heavy work before responding will fail under load, typically during a sale, exactly when it matters.
5. When did someone last look at the logs? With 30 days of retention, a problem that started last month and was never checked is already partly beyond what the dashboard can show.

If your integration was built by someone who is no longer around, collect the access and documentation now rather than during an incident. Our developer handover checklist lists what to get.

How do you recover orders that never synced?

Fix the cause first, then fill the gap, then prove it is closed.

1. Find the start time. The logs show when webhook deliveries began failing, which gives you the window to recover. If it is older than 30 days, use the first missing order in the ERP instead.
2. Restore the subscriptions. Your developer re-registers the webhook topics the app depends on, after fixing whatever made the server fail.
3. Import the missing data. Orders, refunds and stock changes from the gap are pulled from Shopify's API and pushed into the other system. This is the step Shopify's own guidance describes.
4. Reconcile. Compare order counts and totals for the window on both sides. Do not close the incident on the developer's word alone.
5. Add the check that would have caught it. An alert that reaches a person, and a daily reconciliation, turn the next outage into a same day fix.

If orders are missing right now and customers are waiting, treat it as an emergency. Our emergency support guide covers what to check first.

Which integrations are most at risk?

Any custom app that depends on webhooks can lose its subscription, but some setups make it far more likely. Watch for these:

• Apps built for a one-off project. The integration was delivered, the invoice was paid, and nobody was given the job of watching it afterwards. Nothing is wrong until the day something is, and then nobody knows where to look.
• Apps on small or shared hosting. A server that is sized for an ordinary Tuesday may not keep up with the volume of a festive sale, and slow answers count as failures once they pass five seconds.
• Apps that do all their work before replying. The safer pattern is to acknowledge the webhook immediately and process it afterwards. An app that writes to the ERP first and answers Shopify second is the one that times out under load.
• Apps that handle high volume topics. Inventory and order updates arrive in bursts during sales, which is exactly when a fragile integration is pushed past its limits.
• Apps nobody has touched in a year. Shopify retires API versions on a schedule. An app that has not been updated is more likely to start failing on requests it used to make without trouble.

If your integration matches two or more of these, check its logs before the next sale rather than after it.

Is a custom integration still worth it?

Yes, when the need is genuinely specific to your business and a connector app cannot handle it. But a custom app is a running system, not a one-time purchase. It needs someone watching its logs, answering its alerts and updating it when Shopify changes an API. Budget for that from the start, which we explain in our guide to custom app development costs.

The Dev Dashboard does not change that responsibility. It makes it cheaper to carry, because the evidence of a failing integration is now in one place instead of scattered across server logs nobody reads.

Want your integration checked?

Free integration health check. Get in touch or email hello@exactwhy.com with the subject "Integration check", your store URL and what your custom app connects to. We reply within 4 hours and tell you what to look at in the logs, whether your webhooks are at risk, and whether any orders are likely to be missing.

Monitoring and maintenance. If nobody currently owns your integration, we take it over: alerts routed to a person, a daily reconciliation, and fixes when Shopify changes something underneath it.