Running an online store on Shopify means managing a lot more than just sales. One of the most tedious tasks for store owners is accounting and bookkeeping. If done manually, it can take hours each week and lead to errors.
Luckily, Shopify allows seamless automated accounting, helping you save time, avoid mistakes, and stay tax-compliant. With the right tools, you can automate invoicing, profit and loss reports, expense tracking, sales tax calculations, and more.
In this comprehensive guide, you’ll learn how to set up Shopify automated accounting from A to Z — including the best apps, integrations, step-by-step setup, tips, and a full FAQ section.
🚀 Why Automate Shopify Accounting?
✔️ Save Time
No more manual data entry or spreadsheet nightmares.
✔️ Reduce Errors
Automation reduces human mistakes in calculations, reporting, and taxes.
✔️ Stay Tax Compliant
Automated tax reports help you handle local and international tax regulations.
✔️ Get Accurate Financial Insights
Instant profit and loss reports, cash flow statements, and revenue breakdowns.
✔️ Scale Easily
As your store grows, manual accounting becomes impossible. Automation keeps your books clean.
🔧 Step 1: Understand Shopify’s Native Financial Tools
Shopify Provides:
- Basic sales reports (available on Shopify plans and up)
- Payments summaries via Shopify Payments
- Payout reports
- Export CSV files for manual accounting
👉 However, Shopify’s native tools are limited for full accounting needs — like expense tracking, tax filing, bank reconciliation, or generating profit and loss reports.
➡️ That’s where accounting apps and integrations come in.
🛠️ Step 2: Choose the Right Accounting Software
🏆 Most Popular Accounting Tools for Shopify:
| Software | Type | Best For |
|---|---|---|
| QuickBooks | Cloud Accounting | Small to medium businesses |
| Xero | Cloud Accounting | International sellers, scalability |
| Wave | Free Accounting (Limited) | Small stores or beginners (North America) |
| FreshBooks | Cloud Accounting | Freelancers, service-based businesses |
| A2X | Shopify-specific integration | Automating payouts, reconciling sales |
🔗 Step 3: Connect Shopify to Accounting Software
✔️ Direct App Integrations
Visit the Shopify App Store and search for your accounting tool (e.g., QuickBooks, Xero). Apps like QuickBooks Online Sync or Xero Bridge directly connect Shopify to your accounting software.
✔️ Steps to Connect:
- Install the app from the Shopify App Store.
- Log into your accounting software (QuickBooks, Xero, etc.).
- Authorize the connection between Shopify and the software.
- Configure what data to sync:
- Sales
- Taxes
- Refunds
- Shipping income
- Discounts
✔️ Set the Sync Frequency:
- Real-time
- Daily
- Weekly
📊 Step 4: Configure Automated Reports
Key Reports You Can Automate:
- Profit & Loss Statements
- Sales by Product/Region
- Expense Reports
- Cash Flow Statements
- Tax Reports (VAT, GST, US Sales Tax)
Most accounting software offers scheduled reports sent to your email weekly or monthly.
💸 Step 5: Automate Tax Calculations
Tools like:
- TaxJar – For automated US sales tax filing and nexus tracking.
- Avalara – For global tax compliance including VAT, GST.
These apps integrate with Shopify and your accounting software to calculate and report taxes automatically.
🧾 Step 6: Automate Invoices and Billing
- Automatically generate invoices for every sale.
- Send branded invoices to customers via email.
- Store invoice records for tax audits.
Apps for this include:
- Sufio – Automatic Invoices
- Invoice Falcon
- Fakturama (EU VAT invoices)
💳 Step 7: Automate Payment Reconciliation
Shopify payments, PayPal, Stripe — each payout includes fees. Automated accounting tools help you:
- Break down sales, refunds, chargebacks, and fees.
- Match them with bank deposits.
- Avoid manual matching of each transaction.
Apps like A2X are specialized for Shopify payout reconciliation.
🏦 Step 8: Automate Expense Tracking
Connect your business bank account and credit card to your accounting software. It will:
- Categorize expenses (ads, subscriptions, office, etc.) automatically.
- Track recurring charges like Shopify fees, app fees, and advertising.
- Provide real-time expense reports.
🔐 Step 9: Secure Your Data
- Use two-factor authentication (2FA) for all financial software.
- Schedule regular data backups.
- Ensure GDPR/CCPA compliance if dealing with EU or US customers.
🧠 Step 10: Review and Optimize Monthly
- Check monthly reports for anomalies.
- Compare revenue vs. profit — spot overspending.
- Use insights to adjust marketing, pricing, or operations.
🏆 Best Apps for Shopify Automated Accounting
| App | Function |
|---|---|
| QuickBooks Online Sync | Full accounting automation |
| Xero Bridge by Parex | Syncs sales, fees, taxes, and payouts |
| A2X for Shopify | Accurate payout and reconciliation |
| TaxJar | Sales tax automation |
| Sufio | Automatic invoicing |
| Invoice Falcon | Invoice generation |
| Bench | Outsourced bookkeeping + human support |
🔥 Common Mistakes to Avoid
- ❌ Relying only on Shopify’s basic reports for accounting
- ❌ Forgetting to automate tax calculation
- ❌ Not reconciling payment gateway fees (PayPal, Stripe)
- ❌ Skipping monthly financial review
- ❌ Not securing financial data properly
❓ FAQ – Shopify Automated Accounting
🔸 Does Shopify have built-in accounting?
No, Shopify provides basic reports but not full accounting functions like profit & loss, balance sheets, or tax filing.
🔸 Do I need accounting software if I use Shopify?
Yes, to manage taxes, profits, expenses, and accurate reporting, it’s essential to connect Shopify to accounting software like QuickBooks or Xero.
🔸 Is QuickBooks or Xero better for Shopify?
- Use QuickBooks if you prefer wide North American support and integrations.
- Use Xero if you’re international, need multi-currency, and a clean interface.
🔸 Can Shopify handle VAT and GST?
With apps like TaxJar or Avalara, yes. Shopify natively supports basic tax settings but doesn’t automate filings.
🔸 How does A2X help Shopify sellers?
A2X matches Shopify payouts to orders, refunds, fees, and taxes. This ensures your accounting software mirrors your actual bank deposits.
🔸 Can I automate invoices on Shopify?
Yes, apps like Sufio or Invoice Falcon automatically generate and send invoices after every order.
🔸 How often should I check automated reports?
At least monthly for profit checks, but automate weekly if handling high volumes.
🔸 Is automated accounting safe?
Yes, as long as you use reputable apps with secure encryption, regular backups, and 2FA enabled.
🎯 Conclusion
Setting up Shopify automated accounting transforms how you manage your business. You save time, reduce mistakes, gain financial clarity, and scale confidently.
With the right apps like QuickBooks, Xero, A2X, and TaxJar, your Shopify store becomes a fully automated machine — from invoicing to tax compliance.