Shopify QuickBooks Integration: Complete Setup Guide (2025)

Connecting Shopify with QuickBooks eliminates hours of manual bookkeeping and reduces accounting errors. This guide covers the best integration methods, step-by-step setup, and common pitfalls to avoid.

Shopify

integrates with

QuickBooks Online

Accounting 3.7

2025 Integration App Snapshots (Shopify App Store)

Related: Shopify Xero Integration: Automate Your Ecommerce Accounting (2025), Free Favicon Converter.

Sources: A2X on Shopify App Store, QuickBooks Online.

Why Integrate Shopify with QuickBooks?

Manual accounting for ecommerce creates three major problems:

Key benefits of integration:

• Automated order recording - Every Shopify sale creates a QuickBooks invoice or sales receipt
• Accurate tax tracking - Sales tax collected in Shopify maps to QuickBooks tax codes
• Payout reconciliation - Shopify Payments deposits match bank transactions
• Inventory cost tracking - COGS updates automatically with each sale

Integration Methods Compared

Option 1: Third-Party Integration Apps (Recommended)

The most reliable method uses dedicated integration apps from the Shopify App Store.

Our recommendation: A2X for stores over $50K/month revenue, QuickBooks Connector for smaller stores.

Option 2: Zapier or Make (Integromat)

For custom workflows or budget-conscious stores:

Trigger: New Shopify Order
→ Action: Create QuickBooks Sales Receipt
→ Action: Update QuickBooks Inventory (optional)

Pros: Flexible, lower cost for low volume Cons: Requires maintenance, no automatic reconciliation

Option 3: Manual Export/Import

Not recommended for ongoing operations, but useful for:

• One-time historical imports
• Stores with very low order volume (<20/month)

Step-by-Step Setup: A2X Integration

A2X is the gold standard for Shopify-QuickBooks accounting. Here’s the setup process:

Step 1: Install A2X from Shopify App Store

1. Open the A2X listing in the Shopify App Store
2. Click Add app and authorize Shopify permissions
3. Create an A2X account or sign in

Step 2: Connect QuickBooks Online

1. In A2X dashboard, click Connect to QuickBooks
2. Sign in to your QuickBooks account
3. Select the QuickBooks company file to connect
4. Authorize A2X to access QuickBooks

Step 3: Configure Account Mapping

Map Shopify data to QuickBooks accounts:

Step 4: Set Sync Preferences

Configure how transactions post to QuickBooks:

• Summary vs. detailed posting - Summary groups daily sales into one entry; detailed posts each order
• Sync frequency - Daily recommended for most stores
• Historical import - Optionally import past orders

Step 5: Run First Sync and Verify

1. Click Sync Now to process pending transactions
2. Open QuickBooks and verify entries appear correctly
3. Run a Sales by Product report to confirm accuracy

Common Setup Mistakes to Avoid

Mistake 1: Wrong Tax Configuration

Problem: Sales tax posts to income instead of liability Solution: Map tax collected to a liability account (Sales Tax Payable), not income

Mistake 2: Duplicate Entries

Problem: Orders appear twice in QuickBooks Solution:

• Use only one integration app
• Set a clear “start date” for automatic sync
• Disable any manual import processes

Mistake 3: Payout vs. Order Confusion

Problem: Revenue doesn’t match bank deposits Solution: Understand the difference:

• Orders = Gross revenue when sales occur
• Payouts = Net cash when Shopify deposits to your bank

Configure your integration to track both.

Handling Multi-Currency Sales

For stores selling internationally:

Shopify Order (EUR) → QuickBooks (USD)
- Use A2X or Synder (both handle currency conversion)
- Set QuickBooks home currency
- Enable multi-currency in QuickBooks (Plus plan required)

Important: QuickBooks Simple Start doesn’t support multi-currency. You’ll need QuickBooks Plus ($80/month) or higher.

Reconciliation Best Practices

Weekly Reconciliation Checklist

1. Verify Shopify payout matches bank deposit
2. Check that order count matches between Shopify Admin and QuickBooks
3. Review refunds posted correctly as negative revenue
4. Confirm tax collected matches Shopify tax reports

Monthly Closing Process

1. Run A2X settlement report
2. Compare to QuickBooks P&L
3. Investigate any variances > $10
4. Post adjusting entries if needed
5. Reconcile bank account in QuickBooks

Integration Costs Analysis

ROI calculation: If you save 5 hours/month of bookkeeping at $25/hour effective rate, the $29-99/month investment pays for itself.

Troubleshooting Common Issues

Sync Errors

Data Discrepancies

If Shopify and QuickBooks totals don’t match:

1. Check date ranges match exactly
2. Verify all channels sync (POS, online, etc.)
3. Review pending/draft orders excluded from sync
4. Check for manual adjustments in either system

2025 Snapshot

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

Practical Implementation Notes

Data sync and ownership

Most Shopify integrations follow the same lifecycle: a one‑time historical import (customers, products, orders) followed by ongoing incremental updates via API/webhooks. In practice, the biggest failures come from identity and mapping—not from missing features. Before you activate anything customer‑facing, decide which system is the source of truth for customer identity (email vs phone), consent flags, segmentation, and lifecycle fields.

Treat the first week as a controlled rollout. Start with a small segment (internal addresses or a low‑risk cohort), validate that events fire exactly once, and then scale automation volume. This approach prevents silent double‑sending, broken attribution, and hard‑to‑debug “it looks connected but nothing happens” situations.

QA checklist (run once, then reuse)

Use a seed dataset (test customers, a few SKUs, a low‑value test order) to run an end‑to‑end path: signup → first purchase → fulfillment → refund. Confirm that reporting matches your store’s order IDs and timestamps.

Operational checks:

• App permissions/scopes match the features you actually use
• Timezone aligns across scheduled sends, reporting windows, and dashboards
• Edge cases are represented correctly (partial refunds, cancellations, multi‑location fulfillments)
• Baselines are captured so you can measure lift after go‑live

Accounting and ERP workflow notes

Most accounting issues come from mapping. Align tax codes, accounts, and payment fees before you go live. Then validate how refunds, chargebacks, and gift cards are represented. For ERP, plan a short stabilization window after launch—data cleanup is normal.

Practical checks:

• Confirm chart‑of‑accounts mapping for sales, tax, shipping, discounts, and fees
• Decide reconciliation cadence (weekly is usually enough for SMB)
• Validate multi‑currency and rounding behavior (if you sell globally)

Next Steps

Once your Shopify-QuickBooks integration is running:

1. Set up inventory sync for accurate COGS tracking
2. Configure tax automation to simplify sales tax filing
3. Create custom reports combining Shopify and QuickBooks data
4. Train your team on the new workflow

# List the 5 most recent orders (GraphQL)
curl -X POST "https://your-store.myshopify.com/admin/api/2025-01/graphql.json" \
  -H "X-Shopify-Access-Token: $SHOPIFY_ADMIN_TOKEN" \
  -H "Content-Type: application/json" \
  -d "{\"query\":\"{ orders(first: 5, sortKey: CREATED_AT, reverse: true) { edges { node { id name createdAt totalPriceSet { shopMoney { amount currencyCode } } customer { email } } } } }\"}"

Sources

• QuickBooks Online on Shopify App Store
• Shopify: Ecommerce accounting guide
• Shopify: Online payments guide