WooCommerce QuickBooks Integration: Automate Your Accounting (2025)

Manual bookkeeping for WooCommerce stores wastes hours every week and introduces costly errors. Integrating WooCommerce with QuickBooks automates your accounting, giving you accurate financials without the data entry headache.

WooCommerce

integrates with

QuickBooks

Accounting 4.5

Why Integrate WooCommerce with QuickBooks?

Related: Shopify QuickBooks Integration: Complete Setup Guide (2025), WooCommerce QuickBooks Sync: What Data Transfers (Orders, Customers, Products) (2025), Free Favicon Converter.

Running a WooCommerce store without automated accounting creates predictable problems:

Integration benefits:

• Automated sync - Orders flow directly to QuickBooks as sales receipts or invoices
• Accurate tax records - Sales tax maps correctly to QuickBooks tax codes
• Real-time visibility - See daily revenue without waiting for bookkeeping
• Payment reconciliation - Match Stripe/PayPal deposits to orders automatically

QuickBooks Online vs Desktop: Which to Integrate?

Related: Shopify QuickBooks Online Sync: What Data Transfers (Orders, Customers, Products) (2025), Shopify QuickBooks Online Automations: 10 Practical Workflows to Use (2025), Shopify QuickBooks Online Integration Pricing: Cost, Plans & ROI (2025).

QuickBooks Online (QBO)

Pros:

• More integration options available
• Real-time sync capabilities
• Cloud-based (accessible anywhere)
• Regular feature updates

Cons:

• Monthly subscription ($30-200/month)
• Some limitations on customization
• Internet dependent

QuickBooks Desktop

Pros:

• One-time purchase option
• More powerful reporting
• Better for complex inventory
• Works offline

Cons:

• Fewer integration plugins
• Sync often requires local computer running
• Less frequent updates

Recommendation: QuickBooks Online for most WooCommerce stores. Desktop only if you have specific inventory or reporting requirements.

Integration Plugin Comparison

Related: WooCommerce Xero Integration: Sync Your WordPress Store Accounting, Shopify Reviews Apps: Product Review Integration Guide (2025), Shopify Inventory Management Apps: Complete Guide (2025).

Top WooCommerce QuickBooks Plugins

Feature Comparison

Step-by-Step Setup: MyWorks Sync

MyWorks is the most popular WooCommerce-QuickBooks integration. Here’s how to set it up.

Step 1: Install the Plugin

1. In WordPress admin, go to Plugins → Add New
2. Search for “MyWorks Sync for WooCommerce”
3. Click Install Now then Activate
4. Navigate to MyWorks Sync in the admin menu

Step 2: Connect QuickBooks Online

1. Click Connect to QuickBooks
2. Sign in to your Intuit account
3. Select the QuickBooks company to connect
4. Authorize MyWorks access

Step 3: Configure Account Mapping

Map WooCommerce data to the correct QuickBooks accounts:

Step 4: Set Sync Preferences

Configure how orders sync to QuickBooks:

Sync Timing:

• Real-time (recommended for most stores)
• Scheduled (every 15 min, hourly, daily)
• Manual (trigger syncs yourself)

Transaction Type:

• Sales Receipt (for immediate payment)
• Invoice (for payment terms)

Customer Handling:

• Create new customers for each order
• Match by email (recommended)
• Use single “WooCommerce Sales” customer

Step 5: Map Products and Tax

Product Mapping Options:

1. Auto-create products - Plugin creates QuickBooks items automatically
2. SKU matching - Match by SKU (requires consistent SKUs)
3. Manual mapping - Map each WooCommerce product to QuickBooks item

Tax Mapping:

• Map WooCommerce tax classes to QuickBooks tax codes
• For US stores, map to appropriate state sales tax
• For international, configure VAT/GST codes

Step 6: Test and Verify

Before going live:

1. Create test order in WooCommerce
2. Verify sync - Check it appears in QuickBooks
3. Review mapping - Amounts, taxes, fees correct?
4. Test refund - Process refund, verify credit memo

Alternative Setup: A2X (Accountant-Preferred)

A2X takes a different approach, syncing settlements rather than individual orders.

Why A2X is Different

Standard Integration:
Order 1 → QuickBooks Sales Receipt
Order 2 → QuickBooks Sales Receipt
Order 3 → QuickBooks Sales Receipt
...
(Hundreds of transactions)

A2X Approach:
Daily Summary → Single QuickBooks Journal Entry
├── Gross Sales: $5,000
├── Discounts: -$200
├── Refunds: -$150
├── Shipping: $300
├── Sales Tax: $400
├── Payment Fees: -$140
└── Net Deposit: $5,210

Benefits of A2X:

• Cleaner books (fewer transactions)
• Matches bank deposits exactly
• Easier month-end reconciliation
• Preferred by ecommerce accountants

Drawbacks:

• No real-time visibility
• Can’t drill into individual orders in QuickBooks
• Learning curve for summary approach

A2X Setup Steps

1. Create A2X account at a2xaccounting.com
2. Connect WooCommerce (via API or plugin)
3. Connect QuickBooks Online
4. Configure account mapping (similar to above)
5. Set posting schedule (daily recommended)
6. Review first few summaries manually

Handling Common Scenarios

Multi-Currency Orders

If you sell internationally:

1. Enable multi-currency in QuickBooks

   • Requires QuickBooks Plus or Advanced
   • Settings → Company → Currencies

2. Configure plugin currency settings

   • Map each WooCommerce currency to QuickBooks
   • Set exchange rate handling

3. Review currency gains/losses

   • Plugin typically creates adjustment entries

Payment Gateway Fees

Track fees correctly:

Order: $100.00
├── Stripe fee: $3.20
├── Net deposit: $96.80
└── Recording options:
    a) Gross amount as income, fee as expense
    b) Net amount only (not recommended)

Most plugins support option (a), which gives you visibility into true payment costs.

Refunds and Returns

Configure refund handling:

Inventory Sync

If you track inventory in QuickBooks:

1. Enable inventory tracking in QuickBooks
2. Map products to QuickBooks inventory items
3. Set sync direction:
   • WooCommerce → QuickBooks (sales reduce inventory)
   • QuickBooks → WooCommerce (optional stock sync)
4. Configure initial quantities

Warning: Two-way inventory sync can cause conflicts. Most stores should let WooCommerce be the stock master or use dedicated inventory software.

Troubleshooting Common Issues

Issue: Orders Not Syncing

Possible causes:

1. Plugin license expired
2. QuickBooks connection lost
3. Mapping validation errors

Solutions:

• Check plugin status page for errors
• Reconnect QuickBooks if needed
• Review error logs for specific issues

Issue: Duplicate Entries

Possible causes:

1. Multiple sync methods running
2. Manual import + automatic sync
3. Plugin re-syncing old orders

Solutions:

• Use only one integration method
• Set sync start date to avoid historical orders
• Check for duplicate invoices by order number

Issue: Tax Amounts Don’t Match

Possible causes:

1. Tax code mapping incorrect
2. Rounding differences
3. Tax-inclusive vs exclusive pricing

Solutions:

• Verify tax mapping in plugin settings
• Check QuickBooks tax code configuration
• Review WooCommerce tax settings

Issue: Bank Deposits Don’t Reconcile

Possible causes:

1. Payment fees not recorded
2. Timing differences (order date vs deposit date)
3. Currency conversion differences

Solutions:

• Enable payment fee tracking
• Use settlement-based sync (A2X) for easier reconciliation
• Set up proper clearing account workflow

Best Practices

Daily Tasks

• Review sync status dashboard
• Check for any failed syncs
• Verify yesterday’s orders synced correctly

Weekly Tasks

• Reconcile bank deposits to QuickBooks
• Review any manual adjustments needed
• Check for duplicate customers

Monthly Tasks

• Run WooCommerce vs QuickBooks revenue comparison
• Reconcile sales tax collected
• Review payment fee expenses
• Generate P&L and verify accuracy

Year-End Tasks

• Verify all orders synced for the year
• Reconcile 1099 reporting for payment processors
• Review inventory valuations
• Prepare for accountant review

Cost Comparison

ROI calculation: If you save 10 hours/month at $30/hour effective rate, the $39/month plugin pays for itself 7x over.

2025 Snapshot

Quick benchmarks for the QuickBooks workflow. Use these as planning ranges, then validate against your own data.

Next Steps

After setting up WooCommerce-QuickBooks integration:

1. Monitor for 2 weeks - Verify accuracy of synced data
2. Train your team - Ensure everyone understands the workflow
3. Set up reports - Create QuickBooks dashboards for revenue tracking
4. Consider additional integrations - Payment reconciliation, inventory

# List the 5 most recent orders (REST)
curl -u ck_your_key:cs_your_secret \
  "https://example.com/wp-json/wc/v3/orders?per_page=5&orderby=date&order=desc"

Sources

• MyWorks: WooCommerce + QuickBooks
• Shopify: Ecommerce accounting guide
• Shopify: Online payments guide

Need similar integration for Shopify? Check our Shopify QuickBooks integration guide. For more advanced accounting needs, see WooCommerce Xero integration.