Reconciliation Guide

How to reconcile Shopify payouts with LedgerBridge

LedgerBridge posts a balanced journal entry for every Shopify payout. This guide explains what happens after the journal entry is posted, and how to complete the reconciliation in your accounting platform.

The steps differ depending on your posting method (clearing account vs. bank account) and your accounting platform (Zoho Books, QuickBooks Online, or Xero).

Understanding the journal entry

Each journal entry LedgerBridge creates contains line items for every component of the payout:

  • Gross sales (credit) — Revenue before discounts, shipping, and taxes
  • Processing fees (debit) — Card processing fees charged by Shopify Payments
  • Returns & refunds (debit) — Amounts returned to customers
  • Taxes collected (credit) — Sales tax, VAT, or GST collected at checkout
  • Shipping income (credit) — Shipping charges collected from customers
  • Discounts (debit) — Discount amounts applied to orders
  • Shopify payout (debit) — The net deposit amount going to your bank or clearing account

The entry always balances: total debits equal total credits. The Shopify payout line is the balancing amount — it equals the net deposit Shopify sends to your bank.

Additional line items

Depending on your store's activity, you may also see:

  • Shopify fees — Platform fees beyond processing
  • Refund fees — Fees retained when processing refunds
  • Gift card sales — Liability created when gift cards are sold
  • Gift card payments — Liability relieved when gift cards are redeemed
  • Reserves held / released — Funds held back or released by Shopify
  • Capital repayment — Shopify Capital deductions
  • Custom transaction types — Shipping labels, chargebacks, billing charges, and other types you've mapped in the Account Mappings page

Posting method: Clearing account

With the clearing account method, LedgerBridge posts the payout amount to an intermediate clearing account (e.g., "Shopify Payout Clearing"). When the actual bank deposit arrives, you record a transfer from the clearing account to your bank account. This zeroes out the clearing account and completes the reconciliation.

Why use a clearing account?

  • The journal entry and the bank deposit are separate events — the clearing account bridges them
  • Easier to spot discrepancies: if the clearing account doesn't zero out, something needs attention
  • Recommended for most merchants, especially those with an accountant or bookkeeper

Zoho Books — Clearing account steps

  1. LedgerBridge posts the journal entry. The Shopify payout line debits your clearing account (e.g., "Shopify Payout Clearing").
  2. When the bank deposit appears in your bank feed, go to Banking in the left sidebar.
  3. Select the bank account that received the deposit.
  4. Find the Shopify deposit transaction in the statement lines.
  5. Click the transaction, then select Transfer Funds.
  6. Set the "From" account to your clearing account (e.g., "Shopify Payout Clearing").
  7. Confirm the amount matches and save.
  8. The clearing account should now show a zero balance for that payout.

QuickBooks Online — Clearing account steps

  1. LedgerBridge posts the journal entry. The Shopify payout line debits your clearing account.
  2. When the bank deposit appears in your bank feed, go to Banking (or Transactions > Bank transactions).
  3. Find the Shopify deposit in the "For Review" tab.
  4. Click the transaction, then select Record as transfer.
  5. Set the transfer account to your clearing account.
  6. Confirm the amount matches and save.
  7. The clearing account balance should net to zero for that payout.

Xero — Clearing account steps

  1. LedgerBridge posts the manual journal. The Shopify payout line debits your clearing account.
  2. When the bank deposit appears in your bank feed, go to Accounting > Bank accounts.
  3. Click on the bank account that received the deposit.
  4. Find the Shopify deposit in the statement lines.
  5. Click Transfer and select the clearing account as the source.
  6. Confirm the amount and reconcile.
  7. The clearing account should zero out for that payout.

Posting method: Bank account

With the bank account method, LedgerBridge posts the payout amount directly to your bank account. When the actual bank deposit arrives, you match it to the existing journal entry. There's no intermediate account.

Why use bank account posting?

  • Simpler — one fewer account to manage
  • Works well when deposits and payouts arrive on predictable schedules
  • Best for merchants who do their own bookkeeping and prefer fewer steps

Zoho Books — Bank account steps

  1. LedgerBridge posts the journal entry. The Shopify payout line debits your bank account directly.
  2. When the bank deposit appears in your bank feed, go to Banking.
  3. Select the bank account.
  4. Find the Shopify deposit transaction.
  5. Click the transaction. Zoho should suggest matching it to the journal entry based on the amount and date.
  6. Select Match and confirm.
  7. The transaction is now reconciled.

QuickBooks Online — Bank account steps

  1. LedgerBridge posts the journal entry. The Shopify payout line debits your bank account directly.
  2. When the bank deposit appears in your bank feed, go to Banking.
  3. Find the Shopify deposit in the "For Review" tab.
  4. QBO should suggest a match to the existing journal entry. If it does, click Match.
  5. If no match is suggested, click the transaction, select Find match, and search by amount or date.
  6. Select the journal entry and confirm.

Xero — Bank account steps

  1. LedgerBridge posts the manual journal. The Shopify payout line debits your bank account directly.
  2. When the bank deposit appears in your bank feed, go to Accounting > Bank accounts.
  3. Click the bank account.
  4. Find the Shopify deposit. Xero should suggest matching it to the journal.
  5. Click OK to reconcile.
  6. If no match is suggested, click Find & Match and search by amount.

Month-end splitting

When a Shopify payout includes transactions from two calendar months (e.g., sales from March 28-31 and April 1-2), LedgerBridge splits them into separate journal entries — one for each month. This keeps your monthly revenue, fees, and tax figures accurate.

You'll see two entries with reference numbers like PAYOUT-12345-2026-03 and PAYOUT-12345-2026-04. Each entry's payout line represents that month's portion of the total deposit. Reconcile each month's entry against the corresponding portion, or reconcile the total deposit against both entries together.

Troubleshooting

The clearing account doesn't zero out

This means either the journal entry amount doesn't match the bank deposit, or the transfer wasn't recorded. Check the journal entry in LedgerBridge's Activity page and compare the payout amount to the bank deposit. Small differences (under $0.02) are rounding and are handled automatically.

The bank feed doesn't suggest a match

This usually happens when the deposit date differs from the journal entry date by more than a few days. Use the "Find match" or manual search feature in your accounting platform and search by amount.

I see unexpected amounts in the Adjustments line

Adjustments captures transaction types that aren't mapped to a specific account. Go to Account Mappings in LedgerBridge and check the "Your transaction types" section — you may have unmapped types that can be assigned to more specific accounts.