Summary Sync: Square Clearing Account Reconciliation Guide

Synder syncs sales, refunds, payouts and fees from Square. In the Summary Sync mode, transactions are recorded in your accounting platform as summarized journal entries.

This guide explains how to:

  • Identify the ending balance of your Square account in the Summary sync mode
  • Reconcile your clearing account
  • Compare Square and accounting data to identify discrepancies

Use this guide if:

  • You use Square with Synder
  • You use Synder in Summary Sync mode
  • Your clearing account does not reconcile or zero out automatically
  • You want to verify that Square and accounting records match

After completing the steps, your Square clearing account will reconcile with sales, payouts, and fees reflected accurately in your books.

Main Reconciliation Flow

To reconcile your Square clearing account, we need to figure out the ending balances in your Square account. Knowing your ending balance gives you a clear reference point for matching your QuickBooks Online accounts. 

Here’s how you can find the Square balance by downloading Sales Summary and Transfers reports:

Step 1: Access Square Sales Summary Report

  1. Navigate to Square Dashboard
  2. Go to Reports tab. 
  3. Open Sales Summary
  4. Select the required time period
  5. Check Net Total row (This includes all your sales, including cash and check)

Net Total row in the Sales Summary for the period will show you the net sales total after deducting any applicable fees.

We need to subtract the cash and check totals shown under the same report to get the net total of your online sales

Step 2: Adjust for Payouts

Square does not offer a downloadable payout report. Because of this, to match the ending balance numbers, subtract the total funds paid out from the net sales. To access payout/transfers report, follow these steps:

  1. Go to Square Dashboard
  2. Click Balance
  3. Click Activity
  4. Select tab Transfers
  5. Set the same date range as for Sales Summary report
  6. Sum up the payouts to get the total. 

At the final step, subtract the total of transfers from the net sales total. The result is the Square ending balance for the reconciliation period.

Next, compare this amount with the ending balance from your clearing account report in Synder for the same date:

  1. Navigate to Reporting→ Balance sheet.
  2. Select Balance Sheet.
  3. Select column display to Months.
  4. Locate the Square clearing account for the reconciled month.
  5. Subtract the previous month’s balance.

Alternatively, you can check the Balance Sheet report with the monthly column display directly in QuickBooks. 

The result is the clearing account balance for the selected period.

Congratulations! The amounts you will see in the QuickBooks Online Balance sheet report for the clearing account will match your Square ending balance, meaning the reconciliation was successful.

If your Clearing Account does not reconcile

If the balances between your Square and QuickBooks reports don’t match, it’s often caused by unsynchronized transactions. Follow the steps below to make sure that Synder has successfully synced your Square data.

  1. Go to Synder and filter transactions by status. Make sure that all the transactions within your reconciliation period are in statuses: Synced or Skipped on the Platform transactions page.
    All the other statuses indicate that the transaction is not in your books or needs additional checking. As long as such transactions are present, your books won’t reconcile.
  2. Make sure all Square locations are connected.
  3. Make sure you are comparing the right numbers (sales might not equal cash, for example). It’s important to use the right numbers for reconciliation and comparison.
  4. If your platform was disconnected within the reconciliation period, make sure you run a Historical Import on the Platform transactions page to retrieve any missing transactions.

If after that your balances still don’t match, follow the steps below to identify discrepancies by comparing Square and QuickBooks Online data in Excel.

Step 1: Download Required Reports

Download Square Transactions report by following these steps:

  1. Go to Square Dashboard
  2. Locate Transactions 
  3. Set the required date range
  4. Click Export

This downloadable report includes individual transaction details, fees, refunds, and processing information that can be imported into accounting software. The report doesn’t contain the payouts.

You will also need a report of the Square clearing account. In Synder summary sync mode, the transactions are recorded in your accounting platform as summarized Journal Entries. Because of this, Square clearing account report in QuickBooks Online will not include the granular data for each balance transaction. Use Synder Register tab to prepare the clearing account report instead. 

  1. Access the Register page from the left-side menu in Synder
  2. Select the needed Square integration
  3. Select the Clearing accounting category 
  4. Set the same date range
  5. Download report

Please note that Square integration will have 3 separate accounts for your online, cash, and check sales. Select the one you are reconciling under the account subtype

Step 2: Prepare your Excel data for comparison

How to prepare Square Transactions report

Square report includes a lot of transaction details that you don’t need for comparison. Copy values of payment ID and Net Total columns into a new sheet. This will be our Square clean report.

Here’s an example of how it should look like.

How to prepare Clearing Account report

The clearing account report exported from Synder Register tab also includes details that you don’t need for comparison. You only need the Transaction ID and Home Currency Amount columns. However, first, we need to remove payout (transfer) entries and any empty cells.

You can do this by filtering the Transaction type column.

Copy values of Transaction ID and Home Currency Amount columns into a new sheet. This will be our clearing account clean report.

Here’s an example of how it should look like.

Step 3: Consolidate Multiple Lines into One Entry Per Transaction

Square transactions may appear as multiple line items in the Clearing account report (e.g., one per product or fee). For accurate reconciliation, you need to consolidate these into a single row per transaction, showing the total amount. Use Excel’s Consolidate function:

  1. Click on an empty cell in an empty row.
  2. Go to Data → Consolidate.
  3. In the reference box, select both columns A and B (your ID and amount columns).
  4. In the Use labels in the section, check BOTH boxes:
    1. ☑️ Top row (uses column headers);
    2. ☑️ Left column (uses IDs as grouping criteria)
  5. Click OK.

As a result, Excel will group multiple transactions with the same ID into one and sum their amounts.

Step 4: Organize your data

1. Create separate worksheets for:

  • Square original report data
  • Clearing account report data 
  • Comparison Analysis (your working sheet)

2. In your Comparison Analysis sheet, create columns for:

  • Square payment ID
  • Square Amount
  • Clearing account Transaction ID
  • Clearing account Transaction Amount 
  • Lookup
  • Difference

Here’s how the end result should look:

Step 5: Compare data using VLOOKUP

Our objective is to match transaction amounts from Square and the clearing account entries that have shared IDs. This process helps us identify any discrepancies in amounts or missing transactions within the clearing account.

1. Set up your comparison formula

  1. Copy your Square IDs and amounts to columns A and B.
  2. In the Lookup column, use VLOOKUP to find matching Clearing account amounts:

=VLOOKUP(A2,C:D,2,FALSE)

Where:

  • A2 = Square payment ID you’re looking up
  • C:D = Your Clearing account data range (ID in column C, amount in column D)
  • 2 = Returns the amount from the 2nd column (Clearing account amount)
  • FALSE = Exact match only

In the Difference column, calculate the difference by subtracting the looked-up amount from the Square amount. 

2. Identify discrepancies

Perfect matches should show 0 in the difference column.

Common discrepancy indicators include:

  • Negative number = Clearing account amount is higher than the Square amount.
  • Positive number = Square amount is higher than the Clearing account amount. 
  • N/A = Transaction ID exists in Square but not in the corresponding clearing account.

Step 6: Address Common Discrepancies

1. Missing transactions in QuickBooks Online

Possible causes:

  • Transaction failed to sync due to network issues
  • Transaction filtered out by Synder settings
  • Unsupported transaction type
  • Pending/Open Square orders

Actions to take:

  1. Check Synder’s sync logs for failed transactions.
  2. Force a manual sync in Synder for the missing period.
  3. Upon syncing initially missed transactions, rollback, rebuild and sync corresponding summaries.
  4. Confirm timezone settings match between Square reports (PST/UTC) and Synder.
  5. For pending/open Square orders, wait until transaction is completed in Square. Alternatively, adjust for such occurrence to match balances

2. Amount differences

Possible causes:

  • Currency conversion differences between marketplaces
  • Partial refunds not properly matched to original orders
  • Difference in fee calculations between Square reports and Synder processing

Actions to take:

  1. Check for currency conversions if selling in multiple countries.
  2. Look for reserve balance movements in the same period.
  3. Check for related adjustment entries in subsequent periods.

3. Extra transactions in QuickBooks Online

Possible causes:

  • Manual entries created by your accounting team
  • Duplicate syncing from multiple sync attempts
  • Journal entries or adjustments made outside of Synder
  • Starting balance entries when first setting up clearing accounts

Actions to take:

  1. Check if descriptions indicate manual entry.
  2. Verify transaction source in QuickBooks Online (look for “Synder” in descriptions).
  3. Check for duplicate Square connections in Synder.
  4. Review any manual clearing of account adjustments.

When to reach out to support

Get in touch with support when you’ve identified specific transactions causing issues but can’t resolve them.

What to include in your support request:

  • Reconciliation period (start and end dates)
  • Specific transaction IDs
  • Screenshots of problematic transactions in both Square and QuickBooks Online
  • Summary of your findings (e.g., “Found 5 missing fees totaling $47.50”)
  • Currency/marketplace information if applicable
  • Steps already taken to resolve the issue

Best practices for ongoing reconciliation

Staying on top of your clearing accounts requires consistency. Here are key practices to help you keep your books accurate and your reconciliation process smooth over time:

  1. Reconcile monthly rather than waiting for quarter-end.
  2. Monitor multiple currency clearing accounts if selling internationally.
  3. Keep an eye on alerts in Synder for failed sync transactions/summaries.
  4. Maintain timezone consistency across Square, Synder, and reconciliation periods.
  5. Document any manual entries made to clearing accounts.
  6. Review unsupported transaction types periodically as Synder adds support.

A consistent reconciliation routine saves time, reduces errors, and keeps your financials audit-ready. By following these best practices, you’ll avoid surprises down the line and ensure your clearing accounts stay clean and reliable month after month.

Reach out to Synder Team via online support chat or email with any questions you have – we are always happy to help you! 

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