Last updated: November 13, 2026
The best accounting setup for most Shopify stores in 2027 pairs a general ledger, usually QuickBooks Online or Xero, with a Shopify specific sync tool such as A2X or Synder that turns payouts, fees, refunds and taxes into clean summarised entries. Zoho Books, FreshBooks and Sage Accounting are solid alternatives, Wave suits very small stores, and Webgility suits high volume multichannel sellers.
Shopify payouts bundle sales, fees, refunds, chargebacks and taxes into one deposit, which is why connecting Shopify directly to an accounting system often creates messy books. Below is each tool’s role and best fit.
Best Accounting Software For Shopify In 2027
| Software | Role | Best For | Pricing |
|---|---|---|---|
| QuickBooks Online | General ledger | US small and mid sized businesses | Monthly plans |
| Xero | General ledger | UK, Australia, New Zealand and global sellers | Monthly plans |
| A2X | Payout reconciliation and summaries | Clean books for Shopify and marketplaces | Monthly plans by order volume |
| Synder | Transaction sync and reconciliation | Multi channel and payment processor sync | Monthly plans |
| Zoho Books | General ledger | Businesses on the Zoho suite | Free plan, paid tiers |
| FreshBooks | Invoicing and accounting | Owners who also invoice clients | Monthly plans |
| Sage Accounting | General ledger | UK small businesses | Monthly plans |
| Wave | Free accounting | Very small stores | Free core accounting |
| Webgility | Ecommerce accounting automation | High volume multichannel sellers | Monthly plans |
| Shopify Finance reports | Built in reporting | Basic sales and payout reporting | Included |
1. QuickBooks Online
QuickBooks Online is the most widely used small business accounting system in the US, with a large accountant network and many Shopify integrations. Most US Shopify stores use it as the ledger and add A2X or Synder for clean Shopify data.
It suits US based stores that want the accounting system most bookkeepers already know.
2. Xero
Xero is a leading cloud accounting platform in the UK, Australia and New Zealand, with strong bank feeds and multi currency support. Shopify to Xero connections typically run through A2X or Synder.
Xero suits international sellers and stores outside the US.
3. A2X
A2X reads Shopify and marketplace payouts and posts summarised journal entries to QuickBooks or Xero that match each bank deposit, splitting sales, fees, refunds, taxes and shipping into the right accounts.
A2X is the tool many ecommerce accountants recommend for accurate, easy to reconcile books.
4. Synder
Synder syncs transactions from Shopify, payment processors and other platforms into QuickBooks, Xero and other ledgers, with per transaction or summary sync and reconciliation tools.
Synder suits businesses with many payment sources, such as Stripe, PayPal and Shopify Payments together.
5. Zoho Books
Zoho Books is affordable accounting software with a Shopify integration and tight links to Zoho Inventory and Zoho CRM. A free plan is available for very small businesses.
It suits stores that already use Zoho tools.
6. FreshBooks
FreshBooks combines accounting with strong invoicing and time tracking, and connects to Shopify through integrations.
It fits owners who sell online and also bill clients for services.
7. Sage Accounting
Sage Accounting is a popular choice for UK small businesses, with VAT and Making Tax Digital support and Shopify connections through integrations.
It suits UK stores whose accountants work in Sage.
8. Wave
Wave offers free core accounting software, with paid add ons for payments and payroll.
It suits very small or new stores that need basic books at minimum cost.
9. Webgility
Webgility automates ecommerce accounting for multichannel sellers, syncing orders, fees and inventory from Shopify and marketplaces to QuickBooks.
It suits high volume sellers who want detailed order level data and profitability reporting.
10. Shopify Finance reports
Shopify’s built in finance reports summarise sales, payments, taxes and payouts and can be exported for your accountant.
They are a useful baseline but do not replace a proper ledger once you grow.
One Check Worth Making
Ask your accountant which ledger and sync method they prefer before you connect anything. Decide whether you want summary entries that match deposits, which is how A2X works, or individual transactions, and set up the chart of accounts for fees, refunds and taxes first. Fixing messy synced books later costs far more than setting them up correctly.
Frequently Asked Questions
What is the best accounting software for Shopify?
QuickBooks Online and Xero are the most common ledgers for Shopify stores, usually paired with A2X or Synder to turn Shopify payouts into clean, reconcilable entries.
How do I connect Shopify to Xero?
Most stores connect Shopify to Xero through A2X or Synder, which post summarised or detailed entries for sales, fees, refunds and taxes that match each payout.
Does QuickBooks integrate with Shopify?
Yes. QuickBooks connects to Shopify through several integrations, and many accountants recommend A2X or Synder for accurate payout reconciliation.
Why does Shopify make bookkeeping hard?
Shopify payouts combine sales, fees, refunds, chargebacks and taxes into one deposit, so books need a tool or process that splits each payout into the right accounts.
Is there free accounting software for Shopify?
Wave offers free core accounting and Zoho Books has a free plan for very small businesses, though most growing stores move to paid tools.
Conclusion
Pair QuickBooks Online or Xero with A2X or Synder for clean, reconcilable Shopify books, consider Zoho Books, FreshBooks or Sage depending on your region and tools, and use Webgility for high volume multichannel operations. Agree the setup with your accountant before you connect your store. For inventory systems that feed your accounts, see our list of best inventory management apps for Shopify.
