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Fix Shopify → HubSpot Sync Issues (Not Working, Errors, Duplicates)

🔧 7 Common Issues

Diagnose and resolve common sync problems. We've documented the 7 most common issues, their root causes, and exactly how to fix them. See step-by-step fixes for duplicates, missing fields, rate limit errors, and connection issues.

critical High Frequency

Orders/Data not appearing in HubSpot; status shows 'Suspended'

Also searched as: "Shopify HubSpot orders/data not appearing in hubspot; status shows 'suspended'"

#1 Error Threshold Exceeded 60% likely

📋 How to Diagnose

  1. 1. HubSpot > Settings > Integrations > Connected Apps > Shopify
  2. 2. Look for red 'Suspended' banner (triggers after high % of errors)
  3. 3. Click 'Show Errors' to see blocking pattern (usually phone formatting or missing required fields)

✓ Solution

Fix the root data in Shopify (e.g. standardize phone numbers). Then click 'Resync' in HubSpot settings. Sync will resume immediately.

⏱️ Est. time: 15 min

#2 Historical Data Not Backfilled 30% likely

📋 How to Diagnose

  1. 1. Check order date vs. Integration Install Date
  2. 2. HubSpot does not sync pre-existing data automatically upon install

✓ Solution

HubSpot > Settings > Integrations > Shopify > Advanced > Sync Historical Data > Select date range > Backfill.

⏱️ Est. time: 2 min

View Setup Guide
high High Frequency

Refunded orders still marked as 'completed sale' in HubSpot; refund data not syncing

Also searched as: "Shopify HubSpot refunded orders still marked as 'completed sale' in hubspot; refund data not syncing"

#1 Refund Event Not Triggering Sync 80% likely

📋 How to Diagnose

  1. 1. Shopify Admin > Orders > Select refunded order
  2. 2. HubSpot > Contacts > Find associated contact > Check 'Associated Deals'
  3. 3. Look for deal status (should be 'Refunded' or similar, but may still show 'Won')

✓ Solution

Enable refund webhooks in Shopify. In HubSpot, create custom automation: 'If refund is issued' → update deal to 'Refunded' status or move to 'Lost'. Or use Make to sync refund events manually.

⏱️ Est. time: 20 min

Use Make → →
View Setup Guide
high Moderate Frequency

Sync stops after 'Rate limit exceeded' error; no data syncing for hours

Also searched as: "Shopify HubSpot sync stops after 'rate limit exceeded' error; no data syncing for hours"

#1 HubSpot API Rate Limit Hit 85% likely

📋 How to Diagnose

  1. 1. HubSpot > Settings > Integrations > Connected Apps > Shopify > View Logs
  2. 2. Look for '429 Too Many Requests' or 'Rate limit' errors
  3. 3. Check if other integrations are also running (Slack, Zapier, etc.)

✓ Solution

HubSpot's public API allows 100 requests per 10 seconds per app. Reduce sync frequency or use API flow limits. Contact HubSpot Support for rate limit increase on dedicated accounts.

⏱️ Est. time: 10 min

View Setup Guide
medium High Frequency

Custom Shopify fields not syncing to HubSpot properties

Also searched as: "Shopify HubSpot custom shopify fields not syncing to hubspot properties"

#1 Metafields Not Included in Native Integration 95% likely

📋 How to Diagnose

  1. 1. Shopify Admin > Settings > Metafields > Review custom metafields
  2. 2. HubSpot > Contacts > Properties > Check if corresponding custom properties exist
  3. 3. Test: Create contact in Shopify with metafield value, check if it syncs to HubSpot

✓ Solution

Native Shopify integration only syncs standard fields (name, email, phone, address). For metafields, use Zapier (Professional+ plan ~$100/mo) or Make (~$30/mo) to map metafields to HubSpot custom properties.

⏱️ Est. time: 30 min

Use Zapier → →
View Setup Guide
medium Moderate Frequency

Duplicate records in HubSpot for the same customer

Also searched as: "Shopify HubSpot duplicate records in hubspot for the same customer"

#1 Email Mismatch (Unique Identifier) 90% likely

📋 How to Diagnose

  1. 1. Check the 'Email' field on both records.
  2. 2. If email differs (e.g. proxy email vs real email), HubSpot treats them as separate people.

✓ Solution

Enable 'Auto-merge duplicates' in HubSpot settings. If emails differ, you must manually merge or use a third-party tool to match by Name/Phone (risky).

⏱️ Est. time: 10 min

View Setup Guide
medium Moderate Frequency

Abandoned carts not appearing in HubSpot or appearing late

Also searched as: "Shopify HubSpot abandoned carts not appearing in hubspot or appearing late"

#1 Checkout Recovery App Conflict 70% likely

📋 How to Diagnose

  1. 1. Shopify > Settings > Checkout
  2. 2. Check if you use a 3rd party checkout customization or recovery app
  3. 3. These often hijack the webhook event before HubSpot sees it

✓ Solution

Ensure HubSpot is authorized to read 'Checkouts'. If using a 3rd party checkout, you may need to use Zapier to capture the specific app's webhook instead of Shopify's native one.

⏱️ Est. time: 15 min

View Setup Guide
medium Moderate Frequency

Product names, prices, or inventory data not syncing from Shopify to HubSpot

Also searched as: "Shopify HubSpot product names, prices, or inventory data not syncing from shopify to hubspot"

#1 Native Integration Limited to Order/Contact Data 100% likely

📋 How to Diagnose

  1. 1. Review integration scope in HubSpot settings (usually Contact and Order data only)
  2. 2. Check if Product data is a custom requirement

✓ Solution

Shopify → HubSpot native integration syncs orders and contacts, NOT products. Use Zapier or Make to sync product catalog to HubSpot CRM if needed.

⏱️ Est. time: 45 min

Use Make → →
View Setup Guide

Step 1: Try the Official Integration

Direct connection

Start with the native integration if available. It's usually the most reliable, but may have limitations.

View Setup Guide

Free with your subscription

Step 2: Use Make for Custom Flows

No code automation

Create custom integration workflows with Make's visual designer. It works with almost any API.

Try Make Free →

1000 ops/mo free. No credit card.

Step 3: Self-Hosted with n8n

Full data control

Need complete data privacy? n8n is open-source and self-hostable. Build custom integrations with full control over your data.

Try n8n Free →

Open source. Self-host or cloud. Unlimited ops.

Step 4: Add Human Review

Approval automation

Relay adds human-in-the-loop approvals, Slack/Teams alerts, and conditional logic to your automation.

Try Relay Free →

1000 actions/mo free. No credit card.