Shopify orders not syncing to HubSpot? How to find the missing ones

First: are you looking in the right place?

HubSpot's current Shopify integration puts Shopify orders in HubSpot's Orders object, and abandoned checkouts in Carts. Older versions created Deals, and many guides and workflows still expect them. If you're searching Deals, orders can look missing when they're there. HubSpot also asked merchants to reinstall the integration during 2026, and past orders didn't move across by themselves, so check which version you're on.

Step 1: don't trust "On"

A connection that shows On only means it's connected, not that every order arrived. HubSpot keeps a count, per object, of records that are in sync, failing and excluded. One audit found an integration showing On with thousands of failing records.

• In HubSpot, open the Shopify integration's sync settings (under Connected apps) and look at the counts for orders.
• Open Failing to see the records that aren't syncing, and the reason HubSpot gives for each.
• Look at Excluded too: these are records your sync rules leave out on purpose. Check that's what you want.

Step 2: rule out the orders skipped by design

• Guest checkouts without an email can't be matched to a contact. They may sync without one, or not at all, depending on your setup.
• Your sync rules (which records sync, in which direction) may leave some orders out.
• Field mappings changed in either system can make records fail.

Step 3: check a few orders by hand

Pick five recent Shopify orders, including at least one from a returning customer and one placed as a guest, and search for each in HubSpot's Orders. If one is missing and doesn't appear under Failing or Excluded either, note its order number and time: that's the case to take to HubSpot's support, since nothing in the dashboard explains it.

Step 4: bring the missing ones in

Once you've fixed the cause, HubSpot lets you resync just the failing records. Then check your sample orders again. Fixing the cause doesn't rerun workflows that should have fired when those orders were placed, so decide whether any customers need a follow-up by hand.

Would an automatic check help?

We build small apps that check that one business tool really has what another says it sent, and stay quiet unless it doesn't. We're deciding whether to build one for this: comparing every Shopify order with HubSpot and emailing you about any that never arrived, following your sync rules so it doesn't raise false alarms. If this has happened to you, tell us how often and what it cost. It helps us decide.

HubSpot and Shopify are trademarks of their owners. Quiet Penguin is independent and isn't affiliated with or endorsed by either. This guide draws on HubSpot's knowledge base and merchants' reports; we haven't tested it on our own account yet. Screens and setting names change. If something here doesn't match what you see, tell us and we'll update it.