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Configure Shopify Reconciliation with Webgility Online

This article explains how Webgility Online supports accurate Shopify Payout Reconciliation by posting Journal Entries to QuickBooks Online (QBO). It highlights how this method aligns payouts with bank deposits for clean financial records.

Posting as a Summary Journal Entry

When using Summary as a Journal Entry, Webgility Online posts all orders and refunds into a single journal entry under the default payment processor. This simplifies reconciliation by grouping transactions into easy-to-manage batches.


Payout Batching via Shopify Payments

Once Shopify Payments is connected in Webgility Online:

  • Orders, refunds, and fees tied to Shopify Payments are automatically grouped per Payout ID.

  • These are prepared as Ready to Reconcile batches within QuickBooks Online.

  • Payout batches are determined by your Shopify Payment settings, typically daily, but can also be configured for weekly or monthly payouts.

Note1: For U.S. businesses, payouts are processed at the end of the payout period (minus any disputes or held payments).


Note2: It generally takes up to 72 hours after the payout period closes for funds to be deposited and for the payout data to become available from Shopify.

 Learn more about Shopify payout schedules here

How Webgility Online Manages Payout Data

Once the deposit is finalized and available:

  • Webgility Online downloads the payout data.

  • Orders and refunds are batched by Payout ID and reconciled against the data received.

  • Adjustments (such as withheld fees or other adjustments) are automatically recorded as line items against the selected Product or Sales Income account.

  • Orders and refunds are properly categorized into the associated income and expense accounts based on your settings.

Important to Note:

  • Summary as a Journal Entry is currently limited to Shopify Payments when connected through Webgility Online.

  • If Shopify Payments is not connected, you can still post orders using a daily or weekly journal entry summary, but these will not include automated reconciliation with Shopify Payouts.

Benefits of Using Webgility Online for Shopify Reconciliation:

  •  Accurate reconciliation tied directly to payout deposits
  •  No duplicate entries or manual adjustments required
  •  Clean, automated batching by payout period
  •  Reduces time spent on manual reconciliation in QuickBooks Online