QuickBooks ↔ Shopify

How to Connect Shopify and QuickBooks: Methods, Trade-offs, and Setup

By The QuickBooks ↔ Shopify Guide Team

✓ Reviewed by Certified QBO Advisors Updated October 2025 Methodology & disclosure

This guide compares manual CSV, no-code connectors, accounting-grade apps, and ERPs.

It explains when to choose each, who it's for, and how to set it up.

Written for time-strapped founders and small merchants.

View the comparison table Jump to detailed methods Download Mapping Checklist

📋 Editor's note: How we evaluate integration methods

We test tools and may recommend ones we've found reliable for small merchants. Our rankings are based on accounting accuracy, setup time, and maintenance effort—not affiliate relationships or paid platforms.

For context, I've personally used these methods across different stores to understand what works in practice.

Our evaluation criteria:

  • • Does it handle sales tax correctly?
  • • Can it track COGS and inventory?
  • • Does it create clean, auditable books?
  • • How much ongoing babysitting does it need?

We prioritize solutions that accountants trust and founders can actually maintain.

Works with
Shopify QuickBooks Webgility A2X
Reviewed by Certified QBO Advisors · Updated November 2025

Quick Summary: Method Comparison

Compare key features across integration methods to find the right fit for your business.

🧾 Taxes/fees mapping

Manual CSV ❌
No-code connector ⚠️
⭐ Accounting-grade ✅
ERP ✅

📦 COGS & multi-location inventory

Manual CSV ❌
No-code connector ❌
⭐ Accounting-grade ✅
ERP ✅

📊 Daily batching / audit logs

Manual CSV ❌
No-code connector ❌
⭐ Accounting-grade ✅
ERP ✅

⏱️ Setup time

Manual CSV 🐌 Slow
No-code connector ⚡ Fast
⭐ Accounting-grade ⚡ Fast
ERP 🐌 Slow

💰 Total cost

Manual CSV 💵 Low
No-code connector 💵 Low–Med
⭐ Accounting-grade 💸 Med (highest ROI)
ERP 💸💸 High

Note: Connectors pass events; accounting-grade apps post books.

How we evaluate these methods →
🎯 Choose your approach

Choose by method

Select the integration approach that matches your technical skills, budget, and accounting needs.

🤔 Still deciding?

Find your ideal method in three questions

Answer these three questions to identify which integration method suits your needs:

Find your path in 3 questions

Choose by scenario

Match your business situation to the recommended integration approach:

  • Low or medium volume sales? Pick accounting-grade apps for accurate trade-offs with minimal time investment.

  • High transaction inventory or COGS? Choose accounting-grade apps or an ERP for accurate tracking.

  • Just starting out? Start with manual CSV until volume justifies automation.

  • Operating a marketplace or B2C? Accounting-grade apps handle chargebacks, payouts, and fees.

Step-by-step guides

Follow detailed setup instructions for your chosen integration method:

Recommended tools

These tools are trusted by accountants and Shopify merchants for reliable integrations. Scroll through all 10 options to find the right fit for your business:

Compare all 10 tools

Frequently Asked Questions

Is daily batch processing better than per-order posting?

Batching speeds reconciliation and keeps QuickBooks lean. Per-order is fine at low volume or when you need granular reporting.

How do I track payment gateway fees correctly?

Record gross sales, then fees as expenses against the payout; accounting-grade tools automate this per gateway.

Can I use Zapier for this?

Yes for simple cases, but watch taxes, refunds, and inventory—connectors don't enforce accounting logic.

About this guide

Unbiased guidance for small merchants. We don't hide costs or complexity. Reviewed by certified QuickBooks advisors. Last updated: October 2025.