QuickBooks Online / Ecommerce
QuickBooks Online ecommerce integrations: Shopify, Amazon and WooCommerce sales in your books
Short answer. If you just need payouts, fees and refunds reconciled, Intuit’s free Shopify connector or A2X’s payout summaries keep the books clean. If you need order-level detail or inventory sync across channels, look at Webgility or Synder’s per-transaction mode. WooCommerce stores should look at MyWorks Sync.
Check before you connect
- Summary or detailSummaries per payout keep QuickBooks small and reconcile easily; per-order detail helps product-level reporting but adds volume.
- Payout matchingYour bank receives net payouts; check the integration records sales, fees and refunds so the deposit matches.
- InventoryMost payout tools do not touch inventory; if QuickBooks tracks stock, you need an order-level tool or an inventory system.
- HistoryCheck how far back it imports and whether older orders must be pushed by hand.
Connections, by situation
Shopify, keep it simple
Shopify Connector by QuickBooks
- →Sales, refunds and fees
- →Payouts as deposits
Intuit’s connector imports Shopify sales, refunds, fees and payouts into QuickBooks Online and records payouts as deposits, with up to a year of history.
Watch out: Merchants report it works from payout summaries and does not import inventory.
Clean books for Shopify and Amazon
A2X
- →Summary journal per payout (sales, fees, taxes, refunds)
A2X posts one summary journal per payout with lines for sales, fees, taxes and refunds, split across months when needed, ready to match the bank deposit.
Watch out: Summaries, not per-order detail; Amazon Pay needs a clearing-account workflow.
Multichannel orders and inventory
Webgility
- →Orders as sales receipts, invoices or sales orders
- →Returns and payouts
- ⇄Inventory counts
Webgility posts orders from Shopify, Amazon, eBay and Walmart as sales receipts, invoices or sales orders as often as every 15 minutes, with payout reconciliation.
Watch out: Inventory sync is limited to its Plus and Advanced plans.
Stripe, PayPal and Shopify together
Synder
- →Per-transaction sales, fees and refunds
- →Or summary entries per day/payout
Synder lets you choose per-transaction or summary sync for each source; per-transaction mode syncs Stripe activity hourly.
Watch out: Summary mode drops customer and invoice detail.
WooCommerce stores
MyWorks Sync (WooCommerce)
- →Orders and payments
- →Customers
- ⇄Products and inventory
- →Refunds and fees
MyWorks syncs orders, payments, customers, products, inventory, refunds and fees on a 5- to 60-minute schedule.
Watch out: Only new data syncs by default; older records need a manual push.
Compatibility matrix
| Connection | Built by | Direction | Timing | QuickBooks Online plans | App plans | Region / currency |
|---|---|---|---|---|---|---|
| Shopify Connector by QuickBooks | Built by Intuit | → into QuickBooks | Scheduled: Imports transactions automatically; can import up to one year back. | Not stated on pages checked | Free Shopify app; additional charges may apply | Global guide published |
| A2X | Third-party connector | → into QuickBooks | On each event: One journal per payout, split in two when a payout spans months. | Not stated on pages checked | Priced by channel and volume | Not stated |
| Webgility | Third-party connector | ⇄ both ways | Scheduled: Order posting as often as every 15 minutes (vendor). | Not stated on pages checked | Inventory sync on Plus and Advanced plans only | Not stated |
| Synder | Third-party connector | → into QuickBooks | Scheduled: Per-transaction mode syncs hourly for Stripe (vendor). | Not stated on pages checked | Not stated | Not stated |
| MyWorks Sync (WooCommerce) | Third-party connector | ⇄ both ways | Scheduled: Every 5, 10, 30 or 60 minutes for QuickBooks Online. | All QuickBooks Online versions | Free Launch plan; paid tiers by order volume | Not stated |
→ into QuickBooks Online · ← from QuickBooks Online · ⇄ both ways · ? not stated. Directions are per object in the cards above; the matrix shows the overall pattern.
Documented limits
| Connection | Limits the vendor documents |
|---|---|
| Shopify Connector by QuickBooks | Merchant reports and Intuit community posts say it works from summarised payout data and does not import inventory. |
| A2X | Amazon Pay has no direct feed and needs a clearing-account workflow. Summaries, not per-order detail. |
| Webgility | Vendor pages differ on whether QuickBooks or the channel is the master catalogue. |
| Synder | Summary mode does not transfer customer or invoice detail. |
| MyWorks Sync (WooCommerce) | Syncs new data by default; older records must be pushed manually. |
Start from how you report
If you report revenue by channel and month, summaries per payout are enough and keep QuickBooks fast. If you report margin by product or need inventory in QuickBooks, you need order-level sync and clean SKUs on both sides.
Before you connect
Set up a clearing account for payouts, map fees to an expense account, and decide which date (order, payout or deposit) your books use. Run one month in a sandbox or a test company first.
Sources
| Source | Used for | Checked |
|---|---|---|
| Intuit | Shopify Connector by QuickBooks: what imports, payouts | |
| Shopify App Store | Shopify Connector by QuickBooks: listing | |
| A2X | A2X: summary journals | |
| A2X | A2X: Shopify with QBO | |
| Webgility | Webgility: QBO features and plans | |
| Synder | Synder: modes | |
| Synder | Synder: Stripe sync | |
| WooCommerce | MyWorks Sync (WooCommerce): extension documentation | |
| MyWorks | MyWorks Sync (WooCommerce): FAQs |
Other QuickBooks Online integration guides
- QuickBooks Online CRM integrations: what actually syncs between your CRM and your books
- Expense management integrations for QuickBooks Online: cards, receipts and reimbursements
- Inventory software that integrates with QuickBooks Online: what reaches the books
- Payroll software that integrates with QuickBooks Online: how each one posts payroll
- Time tracking that integrates with QuickBooks Online: for payroll, invoices or both