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Connecting Shopify straight to QuickBooks and letting every order flow in sounds sensible. Then you have 4,000 sales receipts a month, payouts that don't match anything, and fees nowhere. Good e-commerce accounting tools solve this by summarizing: one entry per payout that splits sales, shipping, discounts, refunds, fees and sales tax collected into the right accounts.
The stack
| Piece | What it does | Options |
|---|---|---|
| Accounting system | The general ledger and reports | QuickBooks Online, Xero |
| Connector | Turns each payout into a correct summary entry | A2X, Link My Books, Synder, Webgility |
| Inventory app (if needed) | Units, purchase orders, landed cost, COGS | Inventory apps that sync to your ledger |
| Payment processors | Stripe, PayPal, Shop Pay | Usually covered by the connector, or a clearing account |
The shortlist
1. A2X: best for summary posting from Shopify and Amazon
- What it does: posts each settlement or payout as a summary entry to QuickBooks or Xero, mapped to your accounts, so it reconciles to the bank deposit [1].
- Best for: Shopify and Amazon sellers who want clean, reconcilable summaries.
- Watch for: mapping matters. A wrong mapping repeats every payout.
2. Link My Books: best for Amazon and multichannel sellers wanting guided setup
- What it does: summarizes marketplace and store payouts into QuickBooks or Xero, with guided account mapping [2].
- Best for: sellers on several marketplaces. Compare it head to head in A2X vs Link My Books.
3. Synder: best for sellers wanting transaction-level sync across processors
- What it does: syncs sales and payment data from platforms and processors into accounting software, with options for per-transaction or summary sync [3].
- Best for: businesses that need customer- or product-level detail in the ledger.
- Watch for: per-transaction sync creates a lot of entries. Decide on purpose.
4. Webgility: best for higher-volume sellers with QuickBooks
- What it does: automates e-commerce accounting into QuickBooks, including orders, fees and inventory sync [4].
- Best for: higher-volume multichannel sellers on QuickBooks, including Desktop users.
5. QuickBooks Online: best ledger for most US sellers
- Why: widest choice of connectors and accountants; inventory tracking on Plus and Advanced [5].
- Watch for: QuickBooks' own inventory is basic. Heavier inventory needs a dedicated app.
6. Xero: best ledger for sellers with a Xero accountant or international focus
- Why: good multi-currency on higher plans and strong connector support [6]. Compare: QuickBooks Online vs Xero.
Which stack at which size?
| Your business | Usual best fit |
|---|---|
| One Shopify store, simple products | QuickBooks Online or Xero plus A2X or Link My Books |
| Shopify plus Amazon | Same, with both channels in the connector and a clearing account per channel |
| Many channels, purchase orders, imports | Add an inventory app for landed cost and COGS |
| Wholesale plus DTC | Add invoicing and A/R in the ledger; keep DTC as summaries |
Getting the setup right
Whichever connector you choose:
- Use a clearing account per channel. See our e-commerce chart of accounts.
- Map every line: sales, shipping, discounts, refunds, each fee type, reserves and sales tax collected.
- Record payouts as transfers, not income. Walkthroughs: Shopify payouts, Amazon, Stripe.
- Handle COGS from your inventory records. See inventory and COGS.
- Check the first month line by line before trusting it.
Want someone to run it all? See the best e-commerce bookkeeping services. ABFI's e-commerce accounting sets up and maps the stack, then closes the books monthly.
Keep reading
Sources
- A2X, product website, www.a2xaccounting.com. Checked November 6, 2026.
- Link My Books, product website, linkmybooks.com. Checked November 6, 2026.
- Synder, product website, synder.com. Checked November 6, 2026.
- Webgility, product website, www.webgility.com. Checked November 6, 2026.
- Intuit, QuickBooks Online plans and pricing, quickbooks.intuit.com/pricing. Checked November 6, 2026.
- Xero, US pricing and features, www.xero.com/us/pricing-plans. Checked November 6, 2026.
Questions owners ask
What's the best accounting software for a Shopify store?
QuickBooks Online or Xero, with a connector such as A2X or Link My Books posting each payout as a summary.
Should I sync every Shopify order into QuickBooks?
Usually not. Summary entries per payout are easier to reconcile and keep the ledger readable. Order detail stays in Shopify.
What's the difference between A2X and Link My Books?
Both summarize payouts into your ledger. They differ in supported channels, setup approach and pricing. See our full comparison.
Do I need a separate inventory app?
If you have many products, purchase orders, imports or several warehouses, yes. Simple inventory can live in QuickBooks Plus or Advanced.
Will a connector reconcile my books for me?
No. It posts correct entries. Someone still needs to reconcile accounts and close the month.
Want your stack mapped right the first time?
ABFI sets up e-commerce connectors, clearing accounts and inventory, then closes your books monthly. Start with a complimentary Business Accounting Diagnostic.