We are daily monitoring missing orders from the REST admin orders API.
We have an integration that every 5 min fetches new orders from the admin API, with a time filter (updated_at) looking 5 minutes back.
When we are checking our logs, there are periods where admin API returns an empty order array, even though new orders are coming in the same period.
If we later call the API with the same parameters, the orders are appearing.
For example: a few days ago, on Dec 26th 2025 12:00 PM, our client queried for orders with updated_at: 11:55 AM-12:00 PM, and got blank order array in the response. But if you see the screenshot, there are orders in the same time period.
What is the cause for this issue, and how can we avoid it happening again?
This usually happens due to a short indexing delay on Shopify’s side.
When you query orders using a tight updated_at time range and poll frequently, newly created or updated orders may not be immediately available to the API. During that brief window, the API can return an empty array even though orders exist. Retrying the same request later works because the data has finished propagating.
To avoid this: always keep a small time overlap (10–15 minutes), or use cursor-based syncing (since_id) or GraphQL for more reliable incremental fetching.
We encountered a similar issue many years ago on a handful of stores.
The indexing delay only occurred when a specific fulfillment_status filter was set. So the fix for us was to remove the fulfillment_status parameter from the request and do the filtering for it on our end instead.
