The best ecommerce bookkeeping software is a ledger plus a connector
The best bookkeeping software for ecommerce is a general ledger, Xero or QuickBooks Online, paired with a connector that turns marketplace payouts into entries the ledger can reconcile. The two types do different jobs. A ledger holds your chart of accounts, bank feeds, bills, and tax and financial reports. A connector such as Link My Books, A2X, Synder or Taxomate holds none of that. It reads Amazon, Shopify or eBay payouts and posts them to the ledger.
So the real question is which ledger, and whether you need a connector on top. The manual versus automated guide helps with the second part.
Six ecommerce bookkeeping software options and what each is best at
| Product | Type | Entry plan and price | Strongest documented fit | One limitation |
|---|---|---|---|---|
| Xero | Ledger | Early; check Xero's site for the current price | Stores that want the first-party Shopify integration, which Xero says is free on all its plans | Early allows 20 invoices and 5 bills a month |
| QuickBooks Online | Ledger | Simple Start; check Intuit's site for the current price | Shopify stores, since Intuit says its Shopify connector is included with the subscription | Inventory and class tracking start at the Plus plan |
| Link My Books | Connector | Starter 15 Lite, $20 a month, billed monthly | Payout summaries from eight channels, with history and onboarding included | Posts only to Xero and QuickBooks Online |
| A2X | Connector | Mini, $29 a month, up to 200 orders | Businesses that need NetSuite as well as Xero or QuickBooks Online | Multi-channel plans start at $89 a month |
| Synder | Connector | Basic, $65 a month, or $52 billed yearly | Per-transaction records and payment platforms such as Stripe | Basic history is paid and purchases are non-refundable |
| Taxomate | Connector | Starter, $14 a month, or $12 billed annually | Lowest entry price of the four connectors here, and Wave support | No Shopify to Wave connection |
Both ledgers showed promotional pricing on their US pricing pages on that date, so the table quotes no ledger price; check the current price on Xero's and Intuit's sites.
Choosing between Xero and QuickBooks Online as the ledger
Every connector in the table posts to both ledgers, so the connector does not decide this. Three documented differences can.
- Document limits: Xero Early caps you at 20 invoices and 5 bills a month, and Xero's pricing page says transactions started by app partners may count. A connector that posts one invoice per payout can use that up. The next Xero plan, Growing, shows no such cap.
- Users: QuickBooks Online Simple Start has 1 user, Essentials has 3, and Plus has 5.
- Multiple currencies: on Xero this is included only in Established, the highest of the three plans.
Both vendors publish their own Shopify connectors, and each says its connector comes at no extra charge with the subscription. Those apps are for Shopify. Payouts from Amazon, eBay, Etsy and the other marketplaces are where the paid connectors come in.
Where Link My Books fits and where it does not
Link My Books fits a seller on Amazon, eBay, Etsy, Shopify, Walmart, TikTok Shop, WooCommerce or Square who wants one summary per payout. Its price scales in small steps: $24 a month for up to 200 orders and $47 for up to 1,000 on one channel. It includes a 14-day trial, unlimited users and an onboarding call on every plan.
It does not fit three cases. It is not a ledger, so it cannot replace Xero or QuickBooks Online. It does not post to Wave, NetSuite or QuickBooks Desktop. And it does not create a record per order. At the listed prices it is also not the lowest: Taxomate is $14 a month at 200 orders. See the Link My Books review for the detail.
A recommendation for each type of seller
- Shopify-only store, low volume: a ledger plus the Shopify connector its vendor publishes at no extra charge. Add a paid connector only if deposits do not reconcile.
- Amazon or multi-marketplace seller on Xero or QuickBooks Online: a ledger plus Link My Books or Taxomate. Taxomate lists the lower price; Link My Books adds Square and analytics.
- Seller who wants every order and customer in the ledger: Synder in per-transaction mode.
- Business on NetSuite: A2X.
- Seller on Wave: Taxomate, except for Shopify.
Our alternatives page compares the connectors in more depth, and the multichannel guide covers selling on several channels at once.
Sources used for this page
The facts above come from the pages below, read on 3 October 2026. We have not used these products hands-on. Prices and terms change, so confirm them on the vendor's site before you buy.
- Xero pricing plans (US) — Vendor pricing page · xero.com · checked 2026-10-03
- QuickBooks Online pricing (US) — Vendor pricing page · quickbooks.intuit.com · checked 2026-10-03
- Link My Books pricing — Vendor pricing page · linkmybooks.com · checked 2026-10-03
- Link My Books Pricing (US - USD) — Vendor documentation · help.linkmybooks.com · checked 2026-10-03
- A2X pricing — Vendor pricing page · a2xaccounting.com · checked 2026-10-03
- A2X for Shopify pricing — Vendor pricing page · a2xaccounting.com · checked 2026-10-03
- A2X Multi-channel pricing — Vendor pricing page · a2xaccounting.com · checked 2026-10-03
- Synder pricing — Vendor pricing page · synder.com · checked 2026-10-03
- Taxomate pricing — Vendor pricing page · taxomate.com · checked 2026-10-03
- Shopify by Xero on the Xero App Store (US) — Vendor product page · apps.xero.com · checked 2026-10-03
- QuickBooks Online by Intuit on the Shopify App Store — Independent · apps.shopify.com · checked 2026-10-03
- QuickBooks Shopify integration (Intuit) — Vendor product page · quickbooks.intuit.com · checked 2026-10-03
- Resolving a "Transaction Limit" Error in Xero — Vendor documentation · help.linkmybooks.com · checked 2026-10-03