How to Connect Shopify to QuickBooks with Make.com

Managing e-commerce accounting manually is a time-consuming nightmare. Every order needs to be entered into your accounting system, customer information must be synced, and inventory levels need constant updating. This comprehensive guide shows you how to automate the entire process using Make.com to connect Shopify with QuickBooks.

What This Integration Will Do

By the end of this tutorial, your Shopify store will automatically:

Create QuickBooks customers from new Shopify customers
Generate invoices for paid orders
Update inventory levels in QuickBooks
Record payment transactions automatically
Sync tax information and product details
Handle refunds and cancellations

Time Saved: 5-10 hours per week on manual data entry Accuracy Improvement: 99% reduction in accounting errors Real-time Updates: Instant synchronization between platforms

Prerequisites

What You’ll Need

Shopify store with admin access
QuickBooks Online account
Make.com account (Pro plan recommended for this integration)
Basic understanding of your chart of accounts
45 minutes for initial setup

Before You Start

Backup your data: Export current QuickBooks data as a precaution
Clean up products: Ensure product names and SKUs are consistent between platforms
Set up tax rates: Configure tax settings in both Shopify and QuickBooks
Chart of accounts: Have your income and expense accounts ready

Step 1: Prepare Your Make.com Environment

1.1 Create a New Scenario

Log into Make.com and click “Create a new scenario”
Name it “Shopify to QuickBooks Integration”
Set up a folder structure for organization

1.2 Add Shopify Connection

Search for “Shopify” in the apps list
Click “Add a connection”
Enter your Shopify store URL (yourstore.myshopify.com)
Generate a private app API key in Shopify:
- Go to Apps > Manage private apps
- Create private app with read/write permissions for orders, customers, and products

1.3 Add QuickBooks Connection

Search for “QuickBooks Online” in Make.com
Click “Add a connection”
Authorize Make.com to access your QuickBooks account
Select the correct company file if you have multiple

Step 2: Set Up Order Processing Workflow

2.1 Configure Shopify Trigger

Module: Shopify > Watch Orders Settings:

Connection: Your Shopify connection
Webhook Events: Order paid, Order fulfilled
Limit: 100 (adjust based on your order volume)

Filter Settings:

Only process orders with “paid” financial status
Exclude test orders
Filter by order tags if needed

2.2 Customer Synchronization

Module: QuickBooks Online > Search Customers Purpose: Check if customer already exists

Search Criteria:

Field: Email
Value: Shopify customer email

Module: Router (Create two paths)

Path 1: New Customer

Condition: No matching customer found
Action: QuickBooks Online > Create Customer

Customer Mapping:

Name: {{Shopify.customer.first_name}} {{Shopify.customer.last_name}}
Company: {{Shopify.customer.company}}
Email: {{Shopify.customer.email}}
Phone: {{Shopify.customer.phone}}
Billing Address:
  - Address Line 1: {{Shopify.billing_address.address1}}
  - Address Line 2: {{Shopify.billing_address.address2}}
  - City: {{Shopify.billing_address.city}}
  - State: {{Shopify.billing_address.province}}
  - Postal Code: {{Shopify.billing_address.zip}}

Path 2: Existing Customer

Condition: Customer found
Action: Continue with existing customer ID

Step 3: Product and Inventory Sync

3.1 Product Lookup

Module: QuickBooks Online > Search Items Search By: SKU or Name Purpose: Match Shopify products with QuickBooks items

3.2 Create Missing Products

Module: QuickBooks Online > Create Item (if product not found)

Product Mapping:

Name: {{Shopify.line_item.title}}
SKU: {{Shopify.line_item.sku}}
Type: Inventory
Income Account: Sales Revenue
Asset Account: Inventory Asset
Expense Account: Cost of Goods Sold
Unit Price: {{Shopify.line_item.price}}

3.3 Inventory Update

Module: QuickBooks Online > Update Item Action: Adjust quantity on hand based on Shopify order

Step 4: Invoice and Payment Processing

4.1 Create Sales Receipt

Module: QuickBooks Online > Create Sales Receipt

Sales Receipt Mapping:

Customer: {{Customer.ID}} (from previous step)
Date: {{Shopify.order.created_at}}
Payment Method: {{Shopify.order.payment_gateway_names}}
Reference Number: {{Shopify.order.name}}

Line Items:
For each Shopify line item:
  - Item: {{QuickBooks.Item.ID}}
  - Quantity: {{Shopify.line_item.quantity}}
  - Rate: {{Shopify.line_item.price}}
  - Amount: {{Shopify.line_item.total_price}}

Tax Information:
  - Tax Code: Based on Shopify tax lines
  - Tax Amount: {{Shopify.order.total_tax}}

Shipping:
  - Item: Shipping (create this service item)
  - Amount: {{Shopify.order.shipping_lines.price}}

Discounts:
  - Discount Item: (create discount item)
  - Amount: {{Shopify.order.total_discounts}}

4.2 Handle Payment Recording

Module: QuickBooks Online > Create Payment (if using invoices instead of sales receipts)

Payment Details:

Customer: {{Customer.ID}}
Amount: {{Shopify.order.total_price}}
Payment Method: {{Shopify.order.payment_gateway_names}}
Reference: {{Shopify.order.name}}
Deposit Account: Your bank account

Step 5: Advanced Features

5.1 Refund Processing

Shopify Trigger: Watch Refunds QuickBooks Action: Create Credit Memo or Refund Receipt

Refund Mapping:

Customer: Original customer
Amount: {{Shopify.refund.amount}}
Reason: {{Shopify.refund.note}}
Original Transaction: Reference to original sales receipt

5.2 Tax Handling

For Complex Tax Scenarios:

Create separate tax items in QuickBooks for each tax rate
Map Shopify tax lines to appropriate QuickBooks tax items
Handle tax-exempt customers with conditional logic

5.3 Multi-Currency Support

If selling internationally:

Set up foreign currency in QuickBooks
Use exchange rates from Shopify order data
Create separate workflows for each currency

Step 6: Testing and Validation

6.1 Test Scenario Setup

Create a test order in Shopify
Use a small amount to minimize impact
Process manually in Make.com first

6.2 Validation Checklist

✅ Customer created/found correctly
✅ All line items mapped properly
✅ Tax amounts match between platforms
✅ Inventory quantities updated
✅ Payment recorded accurately
✅ Reference numbers allow tracking

6.3 Error Handling

Common Issues and Solutions:

Missing Products:

Set up auto-creation of QuickBooks items
Use error handling to continue processing

Tax Mapping Errors:

Create default tax items for unknown rates
Log errors for manual review

Customer Duplicates:

Search by multiple criteria (email, phone)
Use name matching as fallback

Step 7: Monitoring and Maintenance

7.1 Set Up Monitoring

Make.com Features:

Enable email notifications for errors
Set up execution history review
Create alerts for failed scenarios

Custom Alerts:

Large order amounts (for manual review)
New payment methods
High refund volumes

7.2 Regular Maintenance Tasks

Weekly Reviews:

Check for processing errors
Verify inventory accuracy
Review new product mappings

Monthly Tasks:

Reconcile totals between platforms
Update tax rates if changed
Review customer data quality

7.3 Performance Optimization

Efficiency Tips:

Use filters to process only necessary orders
Batch small orders for processing
Set up different scenarios for different order types

Troubleshooting Common Issues

Connection Problems

QuickBooks timeout: Increase delay between requests
Shopify rate limits: Add pauses in high-volume scenarios
Authentication errors: Refresh connection tokens regularly

Data Mapping Issues

Currency formatting: Use Make.com formatters
Date formats: Convert Shopify timestamps to QuickBooks format
Special characters: Clean text fields before sending

Inventory Sync Problems

Negative inventory: Set up alerts and manual review
Variant tracking: Map Shopify variants to QuickBooks properly
Bundle products: Handle complex product relationships

Results and Benefits

Immediate Benefits

Time Savings: 5-10 hours per week
Accuracy: 99% reduction in data entry errors
Real-time Updates: Instant financial reporting
Scalability: Handle growth without adding accounting staff

Long-term Advantages

Better Cash Flow Visibility: Real-time financial data
Improved Decision Making: Accurate, timely reports
Audit Trail: Complete transaction history
Compliance: Proper tax and financial record keeping

Next Steps and Advanced Features

Phase 2 Enhancements

Expense Tracking: Integrate Shopify fees and shipping costs
Advanced Reporting: Custom financial dashboards
Multi-store Support: Handle multiple Shopify stores
Marketplace Integration: Add Amazon, eBay synchronization

Professional Services

For complex implementations or custom requirements, consider working with automation specialists who can:

Handle complex tax scenarios
Integrate with additional business systems
Provide ongoing monitoring and optimization
Train your team on advanced features

Ready to implement this integration or need help with complex requirements? Contact our automation experts for a consultation tailored to your specific business needs.

Step-by-Step: Connecting Shopify to QuickBooks with Make.com