Shopify doesn’t do your books. It tracks sales and payouts, but it won’t create journal entries, generate a P&L, or file your taxes.
You need accounting software. And you need a way to get your Shopify data into that software without spending hours on manual entry every month.
This guide covers both: the best accounting platforms for Shopify sellers and the best integration tools that connect Shopify to your books automatically.
Why Shopify Sellers Need Accounting Software
Shopify deposits money into your bank account every few days. Each deposit bundles together:
- Product sales across all your listings
- Customer refunds
- Shopify’s transaction fees (2.9% + 30 cents for online credit cards on the Basic plan)
- Shipping charges collected
- Discounts applied
- Sales tax collected
- Third-party payment gateway fees (if you use PayPal, Klarna, etc.)
Your bank sees one number. Your accounting needs dozens of line items.
Without accounting software, you’re guessing. How much is revenue? How much is fees? What about refunds and taxes? Bad data means inaccurate profit margins, messy tax filings, and no clue whether your store is making money.
Two Types of Software You Need
Here’s something most “best Shopify accounting software” articles gloss over: you likely need two tools, not one.
1. Accounting software (where your books live):
- QuickBooks Online, Xero, or Wave
- This is your chart of accounts, financial statements, tax reports, and bank reconciliation
2. A Shopify integration tool (the bridge):
- Taxomate, A2X, or Link My Books
- This pulls Shopify payout data and creates properly categorized journal entries in your accounting software
Some sellers try to skip the integration tool and manually enter payout data. That works if you process 10 orders a month. Once you’re doing 100+, manual entry becomes a full-time job.
Best Accounting Software for Shopify
1. QuickBooks Online
Best for: Most Shopify sellers, especially US-based
Pricing: Simple Start $35/month, Essentials $65/month, Plus $99/month (30-day free trial)
QuickBooks Online is the most popular choice for Shopify sellers. Invoicing, expense tracking, inventory, tax prep. It does it all.
Why Shopify sellers choose it:
- Largest ecosystem of integrations (Taxomate, A2X, and every other Shopify connector works with QBO)
- Built-in inventory tracking on Plus plan and above
- Automatic bank feed reconciliation
- Strong tax reporting for US sellers
- Your accountant almost certainly knows QuickBooks
Shopify-specific considerations:
QuickBooks has a native Shopify connector. Most sellers find it unreliable. It syncs individual orders rather than payouts. So your bank deposit doesn’t match the sum of synced transactions. A tool like Taxomate fixes this. It matches journal entries to actual bank deposits.
Best paired with: Taxomate or A2X for automated payout imports
2. Xero
Best for: UK/EU sellers, multi-currency stores, teams
Pricing: Starter $20/month, Standard $47/month, Premium $80/month (30-day free trial)
Xero is the main QuickBooks alternative. It dominates in the UK, Australia, and New Zealand. If you sell internationally, Xero is worth a look.
Why Shopify sellers choose it:
- Unlimited users on all plans (QuickBooks charges per user)
- Excellent multi-currency support for international selling
- Clean interface that’s easy to learn
- Over 1,000 app integrations
- Strong in UK/EU/ANZ markets where QuickBooks is less common
Shopify-specific considerations:
Like QuickBooks, Xero’s native Shopify integration is limited. It handles basic order syncing. But it doesn’t break payouts into revenue, fees, and refunds. You’ll want an integration tool for proper accounting.
Best paired with: Taxomate or A2X for payout-level accounting
3. FreshBooks
Best for: Freelancers and solo sellers who do a lot of invoicing
Pricing: Lite $21/month, Plus $38/month, Premium $65/month (30-day free trial)
FreshBooks started as invoicing software and grew into full accounting. Good fit if your Shopify store is one part of a service-based business.
Why Shopify sellers choose it:
- Best-in-class invoicing features
- Simple expense tracking with receipt scanning
- Built-in time tracking (useful for custom/made-to-order sellers)
- Clean mobile app
Limitations for Shopify sellers:
FreshBooks lacks the e-commerce integrations QuickBooks and Xero have. No native Shopify payout connector. Fewer third-party tools support it. If your primary business is your Shopify store, QuickBooks or Xero is the better pick.
4. Wave
Best for: New sellers and side hustles on a tight budget
Pricing: Free (paid add-ons for payroll and payments)
Wave is free. For a new Shopify seller not ready to pay $35-$99/month for QuickBooks, Wave is a solid starting point.
Why Shopify sellers choose it:
- Completely free core accounting
- Unlimited income and expense tracking
- Basic invoicing included
- Financial reports (P&L, balance sheet, cash flow)
Limitations for Shopify sellers:
Wave doesn’t have a native Shopify integration. Most payout connectors don’t support it either. You’ll need to manually import data or build a Zapier workflow. Once you pass ~$5K/month in revenue, the manual work usually justifies upgrading to QuickBooks or Xero with automation.
5. Zoho Books
Best for: Sellers already in the Zoho ecosystem
Pricing: Free (up to 1,000 invoices/year), Standard $15/month, Professional $40/month
Zoho Books is a solid mid-range option. Pricing is competitive. It’s especially attractive if you already use other Zoho products like CRM or Inventory.
Why Shopify sellers choose it:
- Free tier available for small sellers
- Inventory management included
- Built-in Shopify integration that syncs orders every hour
- Multi-currency support
- Automated bank reconciliation
Limitations for Shopify sellers:
Zoho’s Shopify integration syncs orders, not payouts. Your Zoho records won’t match your bank deposits directly. You’ll need manual reconciliation for Shopify’s fees, refunds, and payment holds.
6. Sage Business Cloud
Best for: Growing businesses that want scalability
Pricing: Start $10/month, Standard pricing varies by region
Sage is well-established. It works for Shopify sellers, particularly in the UK and Canada.
Why Shopify sellers choose it:
- Syncs orders, refunds, and customer records from Shopify every 60 minutes
- Cash flow forecasting
- Strong compliance features for UK VAT
- Scales well as your business grows
Limitations for Shopify sellers:
Sage has the same order-level sync problem as Zoho. It imports individual transactions. It doesn’t match to bank-level payouts. High-volume sellers will hit reconciliation gaps.
Best Shopify Integration Tools
These tools solve one specific problem: getting Shopify payout data into your accounting software correctly. They sit between Shopify and QuickBooks/Xero. They create journal entries that match your actual bank deposits.
7. Taxomate
Best for: Multi-channel sellers, budget-conscious stores, sellers who need COGS tracking
Pricing: Starts at $14/month (Starter), $27/month (Multi-channel), $36/month (Inventory Sync)
Supported accounting software: QuickBooks Online, Xero
Taxomate imports your Shopify payouts automatically. It breaks each one into line items: sales, refunds, fees, shipping, taxes, discounts. Each payout becomes a journal entry that matches your bank deposit exactly.
Why Shopify sellers choose it:
- Fastest setup: Connect Shopify and QuickBooks in about 5 minutes
- Payout-level accounting: Journal entries match your bank deposits for one-click reconciliation
- Multi-channel support: If you also sell on Amazon, eBay, Walmart, Etsy, TikTok Shop, or WooCommerce, one Taxomate subscription covers all channels
- Inventory sync: The only integration tool that syncs inventory data to QuickBooks for COGS tracking
- Free historical imports: Pull past payouts at no extra charge
- Cheapest multi-channel pricing: Unlimited channels for one flat rate vs. per-channel billing
Shopify-specific features:
- Handles Shopify Payments and third-party payment gateways
- Automatic “gross-up” accounting (separates the net payout into gross sales minus fees)
- Supports Shopify Plus stores
- Monthly auto-split for payouts crossing month boundaries
Pricing comparison for Shopify sellers:
| Monthly Orders | Taxomate | A2X | Link My Books |
|---|---|---|---|
| Up to 200 | $14 | $19 | $17 |
| Up to 1,000 | $24 | $49 | $33 |
| Up to 5,000 | $44 | $69 | $50 |
| Up to 10,000 | $79 | $99 | $83 |
If you sell on multiple channels, the gap widens. A2X and Link My Books charge per channel. Taxomate’s multi-channel plan includes unlimited channels.
8. A2X
Best for: Sellers whose accountant specifically requires A2X
Pricing: Starts at $19/month for Shopify
Supported accounting software: QuickBooks Online, Xero
A2X does the same core job as Taxomate. It imports Shopify payouts as journal entries. It’s been around since 2014 and has strong adoption among e-commerce accounting firms.
Why Shopify sellers choose it:
- Well-known among accountants and bookkeepers
- Long track record with established reputation
- Handles complex multi-currency scenarios
- Good documentation and support
Compared to Taxomate:
A2X costs more at every tier. It charges per channel. No inventory sync. No free historical imports. But if your accountant knows A2X and prefers it, that matters. Ask them if they’re open to alternatives before deciding.
How to Choose the Right Setup
Your choice depends on three things: your volume, your channels, and your budget.
Solo Shopify store, under 500 orders/month
Recommended: QuickBooks Online Simple Start ($35/month) + Taxomate Starter ($14/month) = $49/month total
Full accounting with automated payout imports. Setup takes under 10 minutes. Once connected, Shopify payouts flow into QuickBooks automatically. Reconcile with one click.
If $49/month is too steep, start with Wave (free) and manually import payout summaries until you’re ready to upgrade.
Growing Shopify store, 500-5,000 orders/month
Recommended: QuickBooks Online Plus ($99/month) + Taxomate Multi ($58/month) = $157/month total
At this volume, you need inventory tracking and proper COGS accounting. QuickBooks Plus handles inventory. If you also sell on Amazon or eBay, Taxomate’s multi-channel plan covers everything for one price.
International Shopify store (UK/EU/ANZ)
Recommended: Xero Standard ($47/month) + Taxomate Starter ($14/month) = $61/month total
Xero’s multi-currency support and UK/EU market dominance make it the natural choice. Your local accountant likely works in Xero already.
High-volume or multi-channel (5,000+ orders/month)
Recommended: QuickBooks Online Plus ($99/month) + Taxomate Inventory ($83/month) = $182/month total
At this scale, COGS tracking across channels is critical. Taxomate’s inventory plan syncs Shopify sales as inventory invoices in QuickBooks. You get SKU-level profitability data.
Enterprise sellers doing 50,000+ orders should consider NetSuite ($499+/month). It includes ERP, multi-location inventory, and advanced reporting. QuickBooks can’t match it at that scale.
The Shopify Accounting Problem Nobody Talks About
Every “best accounting software for Shopify” article lists the same tools and moves on. But the real problem isn’t which software you pick. It’s the data. Shopify’s payout data is messy. Getting it into clean books is the hard part.
Here’s what actually happens:
Say Shopify deposits $4,827.31 into your bank account. Your accounting software sees one number. But that deposit is actually:
- $5,412.00 in gross sales
- -$156.93 in Shopify transaction fees
- -$318.50 in refunds
- -$85.00 in chargebacks ($15 fee each)
- +$124.74 in shipping collected
- -$149.00 in discounts applied
Record $4,827.31 as “Shopify Sales” and your books are wrong. Revenue is overstated. Fees aren’t tracked. Refunds don’t exist in your records. Your tax filing is based on bad data.
This is why integration tools exist. They pull each payout apart. Sales, fees, refunds, taxes. Separate line items. Clean journal entries your accountant can work with.
Getting Started
Here’s the fastest path from zero to working Shopify accounting:
-
Pick your accounting software. QuickBooks Online if you’re US-based, Xero if you’re UK/EU/ANZ. Wave if you’re just starting and can’t afford a subscription yet.
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Pick your integration tool. Taxomate for the best value and fastest setup. A2X if your accountant requires it.
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Connect everything. Taxomate takes about 5 minutes. Connect Shopify, connect QuickBooks or Xero, review your account mappings, import your first payout.
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Set up auto-posting. Enable automatic imports. New Shopify deposits flow into your books without manual work.
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Reconcile. Each payout creates a journal entry matching your bank deposit. Click “match” in your accounting software. Done.
That’s it. No spreadsheets. No manual data entry. Your books stay current with every Shopify payout.
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