Shopify Sales Tax to QuickBooks: Import Guide (2025)

Updated: 2025-01-15 8 min read

Getting sales tax right isn't optional — it's a legal requirement. This guide shows you exactly how to import Shopify sales tax data into QuickBooks so your tax reporting is accurate and audit-ready.

Why Sales Tax Accuracy Matters

Since the 2018 South Dakota v. Wayfair Supreme Court decision, e-commerce sellers have economic nexus obligations in most US states. This means:

You must collect sales tax in states where you exceed threshold (typically $100K sales or 200 transactions)
You must remit that tax to each state
You must keep accurate records for audits

If your QuickBooks data doesn't match what you collected in Shopify, you're at risk for:

Underpayment penalties — Interest + fines on unpaid tax
Audit liability — State auditors can go back 3-7 years
Bookkeeping chaos — P&L and balance sheet errors

How Shopify Exports Tax Data

When you export orders from Shopify, tax data appears in several columns:

Tax-Related Columns in Shopify Export

Column	Description	Example
`Taxes`	Total tax amount for the order	12.45
`Tax 1 Name`	Name of first tax rate	CA State Tax
`Tax 1 Value`	Amount for first tax	8.45
`Tax 2 Name`	Name of second tax (if applicable)	LA County Tax
`Tax 2 Value`	Amount for second tax	2.00
`Tax 3 Name`	Name of third tax (if applicable)	LA City Tax
`Tax 3 Value`	Amount for third tax	2.00

Shopify supports up to 3 tax lines per order. Most US orders have 1-2.

QuickBooks Sales Tax Setup

QuickBooks Online

Before importing, verify your QuickBooks tax settings:

Go to Taxes → Sales Tax → Sales Tax Settings
Ensure "Automatic Sales Tax" is configured for your nexus states
Verify tax agencies are set up correctly

Tax Handling Options

When importing Shopify data to QuickBooks, you have two approaches:

Approach	Pros	Cons
Import as gross amount (Tax included in total)	Simple, fast import	Tax not tracked separately in QBO
Import with tax breakout (Tax as separate line)	Accurate Sales Tax Center reporting	Requires proper tax code mapping

Recommendation: If you use QuickBooks Sales Tax Center for filing, use the tax breakout method.

How We Handle Sales Tax

Our converter preserves tax data from Shopify and formats it for QuickBooks:

Tax Field Mapping

Shopify Field	QuickBooks Field	Notes
`Taxes`	`TaxAmount`	Total tax preserved
`Tax 1 Name`	Memo field	Tax jurisdiction recorded
`Shipping Province`	Used for tax assignment	State-level tax routing

Multi-tax orders are aggregated into a single tax amount for clean import.

Handling Tax-Exempt Orders

Identifying Tax-Exempt Orders

In Shopify, tax-exempt orders show Taxes = 0 even when the order has taxable products. Common scenarios:

Wholesale customers — Resale certificates on file
Non-profit organizations — 501(c)(3) exemptions
Government purchases — Federal/state agency orders
Tax-free states — Orders shipped to OR, MT, NH, DE, AK

QuickBooks Import

Tax-exempt orders import normally with TaxAmount = 0. To maintain audit trail:

Review orders with zero tax but taxable items
Verify exemption reason in Shopify customer notes
Keep exemption certificates on file (QuickBooks Attachments or separate folder)

Multi-State Tax Reporting

If you have nexus in multiple states, you need to report and remit tax to each state separately.

Option 1: QuickBooks Sales Tax Center

After importing Shopify orders with tax amounts:

Go to Taxes → Sales Tax
QuickBooks groups taxable sales by state
File returns directly through QBO (available for most states)

Option 2: Export for Manual Filing

If you use a state's own portal or a service like TaxJar/Avalara:

Export sales by state from QuickBooks
Or use Shopify's tax reports directly
File through the state portal

Option 3: Automated Filing Services

Services like TaxJar AutoFile or Avalara can:

Pull data directly from Shopify
File returns in all nexus states
Handle rate changes automatically

Cost: $20-50/month/state. Worth it if you have 5+ nexus states.

International: VAT and GST

Selling internationally? Tax gets more complex:

UK/EU VAT

Shopify can collect VAT at checkout (for orders under €150 to EU)
VAT appears in the "Taxes" column
QuickBooks Online has VAT-specific settings (enable in Company Settings)

Canada GST/HST/PST

Multiple tax types: GST (federal), HST (combined), PST (provincial)
Shopify handles calculation per province
Import total tax; QuickBooks Canada edition handles breakdown

Australia GST

10% GST on most goods
Shopify collects automatically for AU customers
QuickBooks Australia edition has GST reporting built-in

Tax Reconciliation Checklist

After importing, verify your tax data:

Monthly Reconciliation

Shopify Tax Report: Analytics → Reports → Taxes
QuickBooks Tax Report: Reports → Sales Tax Liability
Compare totals: Should match within $0.01

Common Discrepancies

Issue	Cause	Solution
QBO shows higher tax	Refunds not imported	Import refunds separately
QBO shows lower tax	Orders missing from import	Check date range filters
Rounding differences	Line-item vs order-level rounding	Accept if under $1/month

Ready to import your Shopify tax data correctly?

Convert with Tax Handling

Frequently Asked Questions

No. When you import via CSV, the tax amount from Shopify is used as-is. QuickBooks doesn't recalculate. This is actually what you want — it preserves what you actually collected.

Common causes: missing refunds, date range mismatch, or orders filtered out during export. Run reports for the exact same date range and include all order types.

Not via CSV import. QuickBooks CSV doesn't support multi-jurisdiction tax breakout. For detailed tax tracking, use QBO's automatic tax or a dedicated tax service.

If Shopify is set to tax-inclusive pricing (common in EU/UK), our converter extracts the tax amount. The imported transaction shows the tax-exclusive subtotal plus tax.

For most US sellers under $500K/year, Shopify's built-in tax is sufficient. Above that, or with 10+ nexus states, TaxJar or Avalara provide better automation and audit protection.