📊 Top Accounting Software for Shopify Stores
🔹 Xero
A cloud‑based accounting platform that integrates directly with Shopify using its official connector. It:
- Syncs Shopify sales, fees, and payouts automatically.
- Tracks cash flow and profit in real time.
- Helps reconcile bank transactions with Shopify data. Xero
Best for: Small to scaling ecommerce businesses.
🔹 QuickBooks Online (with Shopify Integration)
One of the most popular accounting tools globally, QuickBooks can be connected to Shopify using apps like Webgility or QuickBooks Connector:
- Automates recording of orders, sales, fees, and taxes.
- Provides robust reporting (P&L, balance sheet, cash flow).
- Excellent for US sellers handling multi-state sales and tax. Rootsyntax Technologies+1
Best for: US‑based merchants needing comprehensive tax and financial reports.
🔹 Synder
Synder specializes in ecommerce accounting automation:
- Connects Shopify with your accounting system quickly (sales, fees, refunds).
- Lets you configure sync rules for different payment methods and sales channels.
- Helps reconcile Shopify payouts without manual data entry. Synder
Best for: Businesses wanting faster setup and automated transaction syncing.
🔹 Seller Ledger
Designed specifically for ecommerce bookkeeping, Seller Ledger:
- Automates capture of Shopify sales (any payment method).
- Tracks order details, refunds, and returns for accurate profit reporting.
- Generates tax‑ready summaries and reports. Seller Ledger
Best for: Sellers who want an ecommerce‑focused accounting solution.
🔹 A2X (Sync Tool)
Not full accounting software by itself, but an essential connector that:
- Breaks down Shopify payouts into matched sales, fees, refunds, and taxes.
- Works with accounting systems like QuickBooks, Xero, Sage, or NetSuite.
- Great for automated reconciliation and clean books. EComposer
Best for: High‑volume sellers or anyone wanting precise payout reconciliation.
🔹 Zoho Books
A budget‑friendly cloud accounting tool with Shopify connections:
- Manages invoicing, expenses, and bank reconciling.
- Connects to Shopify via Zoho Flow or third‑party connectors.
- Supports inventory tracking when linked with Zoho Inventory. Shopify
Best for: Small sellers and startups on a budget.
🔹 Wave (With Integrations)
Free (with optional paid upgrades) accounting software that:
- Offers basic bookkeeping features.
- Can connect to Shopify via Zapier or other connectors.
- Good starting point for solopreneurs or very small stores. Shopify
Best for: Budget‑conscious beginners.
🧠 How These Software Tools Help Shopify Sellers
Automated syncing: Orders, payouts, fees, and refunds flow automatically from Shopify into your accounting system. Shopify Community
Accurate reconciliation: Tools like A2X help match Shopify deposits to accounting records to avoid bookkeeping errors. EComposer
Profitability tracking: Many solutions calculate true profit after fees, shipping, and returns. Seller Ledger
Tax support: Most platforms support sales tax tracking and provide reports your accountant can use for filings. Rootsyntax Technologies
🛠 Tips for Choosing Shopify Accounting Software
- Check native integration: Prefer solutions that sync directly with Shopify or via well‑supported connectors. Xero
- Consider your volume: High‑volume sellers benefit more from automated reconciliation tools (e.g., A2X + QuickBooks/Xero). EComposer
- Look at tax features: US sellers especially need help tracking sales tax and preparing tax returns. Meetanshi – Magento & Shopify Agency
- Budget and scalability: Wave may suit small stores; QuickBooks/Xero are more scalable for complex businesses. Shopify