Webgility Online: Syncing Fees as Net Values in QuickBooks Online
This article helps Webgility Online users switch their QuickBooks Online fee sync from posting fees as separate (gross) transactions to embedding them as line items within each order (net values). It also explains how to verify the change by posting a test order.
Why Fee Sync Settings Matter
When Webgility Online sends your sales data to QuickBooks, you can choose how payment processor fees appear:
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Separate Transaction: Fees post as standalone entries, showing gross amounts.
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Line Item with Order: Fees show up on each order as a separate line item, so QuickBooks reflects the net revenue.
Switching to Line Item with Order gives you a cleaner ledger with actual amounts you received.
How to Update Your Fee Sync in Webgility Online
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Log in to Webgility Online and select the Sync Settings.
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Find the Fees setting.
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Toggle from Separate Transaction to Line Item with Order Transaction.
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Click Save to lock in your new preference.
Verify in QuickBooks Online
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Open QuickBooks Online and find a recently synced order.
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Check that there’s a separate “Fee” line under the order details.
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Confirm the order total matches the net amount you expected.
Run a manual test sync.
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Back in Webgility Online, go to Sales > Orders and click "Post to QuickBooks."
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Wait for the sync to complete, then refresh QuickBooks Online.
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Review your test order to make sure fees are embedded correctly.
Friendly Tips for Smooth Fee Management
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Always re-sync after changes: That way your QuickBooks data updates immediately.
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Start small: Test your setting on one or two orders before syncing a whole batch.
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Keep a screenshot record: Capture your before-and-after views to easily confirm everything’s right.
With your fee sync set to Line Item with Order, QuickBooks Online will show exactly what you pocketed—no more wading through separate fee transactions!