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Shopify Payout Reconciliation with Webgility QuickBooks Connector

This article explains how users can reconcile their Shopify payouts with QuickBooks Online using the Webgility QuickBooks Connector. It provides a step-by-step overview to ensure that sales, fees, and deposits are properly aligned between Shopify, QuickBooks, and the actual bank records. The content walks users through identifying payout details in Shopify, tracing the payout entries within QuickBooks (including sales, fees, and clearing account movements), and matching those entries to real bank deposits for accurate reconciliation. It also emphasizes the importance of verifying that the Shopify Payments Clearing Account has a zero balance after reconciliation, confirming that all transactions have been accurately processed and no funds remain pending. By following this guide, users can ensure that their Shopify payouts are seamlessly recorded and reconciled in QuickBooks, maintaining clean and accurate financial records.

A Simple Guide to Reconciling Shopify Payouts in QuickBooks

When Shopify sends you money, it's called a payout. This payout represents your sales minus any fees or refunds. Reconciling this means ensuring every part of that transaction—the sales, the fees, and the final deposit—is perfectly recorded in QuickBooks and matched to your actual bank activity.

## Step 1: Get Your Payout Details from Shopify 🛍️

Your Goal: To find the specific payout in Shopify and understand its breakdown.

  1. Find Your Payout Report: In your Shopify admin, go to Finances > Payouts. Select the specific payout you want to check.
  2. Identify Key Numbers: On the report, find these three figures:
    • Total charges: The gross sales included in the payout.
    • Total fees: What Shopify charged for processing.
    • Net payout amount: The final amount of cash deposited into your bank.

For example, the August 18th payout, which includes orders from August 13th, shows a total collection of $65.62. After deducting $2.20 in Shopify Payment Gateway fees, the net deposit was $63.42.

  • Check Payout Details (Optional): If you want to see exactly which orders make up that payout, click on the payout itself. This will open a detailed view showing all the individual orders and transactions included.

## Step 2: Trace the Payout Inside QuickBooks 🧾

Your Goal: To see how the different parts of your payout were automatically recorded in your QuickBooks account.

  1. Check the Expenses (Shopify Fees): Shopify fees are a business expense. In QuickBooks, you can see these recorded in an expense account like "Shopify Fees" by running a Transaction Detail by Account report for that account.
  2. See the Money Move (The Clearing Account): Your sales don't go directly to your bank account in QuickBooks. They first enter a "waiting room" called a Clearing Account (e.g., "Shopify Payments Clearing"). The payout transaction then moves the money out of this account, splitting it between your bank deposit and the fees expense.

Following the example, the $65.62 in the Shopify Clearing Account was settled: $63.42 was deposited into the Bank Account (Chase Checking), and the remaining $2.20 was recorded as a Shopify Payment Fees expense.

## Step 3: Match the Deposit in Your Bank Feed 🏦

Your Goal: To connect the QuickBooks transaction with the actual money that arrived from Shopify in your real-world bank account. This is the most important step in bank reconciliation.

  1. Go to Your Bank Feed: In QuickBooks, navigate to the Banking or Transactions tab. Here you'll see a list of recent transactions pulled directly from your synced bank account.
  2. Find the Shopify Deposit: Locate the deposit from Shopify. Its amount should exactly match the Net payout amount from your Shopify report.
  3. Click "Match": QuickBooks is smart and will likely find the deposit transaction that was already created from the payout data. As shown in the image below, it will present a green "Match" option. Clicking this button tells QuickBooks, "Yes, this real-world deposit is the same one we've already accounted for." This confirms the cash is received and prevents you from counting the income twice.

This $63.42 net deposit should then match the corresponding transaction that appears in your bank feed for that account.

## Step 4: The Final Check on Your Balance Sheet ✅

Your Goal: To make sure no money is "stuck" in the clearing account and that everything has been fully accounted for.

  1. Pull Up Your Balance Sheet: In QuickBooks, run the Balance Sheet report.
  2. Check the Clearing Account Balance: Look under the Assets section for your "Shopify Payments Clearing" account. Now that you've matched the payout, the balance in this account should ideally be $0. If there's a balance, it should only be from new sales that haven't been paid out yet.