PayPal Clearing Account Reconciliation Guide for Synder Users – Per Transaction

Synder syncs sales, refunds, payouts, and fees from PayPal. Depending on your settings, these flow into your accounting platform as individual transactions or summarized journal entries.

This guide explains how to:

  • Find out the starting and ending balance of your PayPal account.
  • Reconcile your clearing account
  • Compare data between PayPal and your bookkeeping platform to identify discrepancies

QuickBooks Online is used as an example, but the same reconciliation approach applies to other supported accounting integrations.

Use this guide if:

  • You use PayPal with Synder
  • Your clearing account does not reconcile or zero out automatically
  • You want to verify that PayPal and accounting records match

After completing this guide, your PayPal clearing account will reconcile correctly, with all sales, payouts, and fees accurately reflected in your books.

Main Reconciliation Flow

To reconcile your PayPal clearing account, we need to compare its ending balance with PayPal’s ending balance for the reconciled month.

Here’s how you can find your PayPal balance by downloading the Financial Summary report:

  1. Go to PayPal → Reports→ Payments.
  2. Select Statements.
  1. Choose the reconciliation period range and click Create Report.
  2. Request the CSV version of the report.
  1. Once the report is ready, download it.
  2. Locate the Balance column.
  3. Find the entry for the last day of the month and copy the amount.


Next, compare the amount you copied with the ending balance from your clearing account report in QuickBooks Online for the same date.



The amounts you will see in the QBO clearing report will match your PayPal Statement report amount, meaning the reconciliation was successful. Congratulations!

If Your Clearing Account Does Not Reconcile

If the balances between your PayPal and Quickbooks report don’t match, it’s often caused by unsynchronized transactions. Follow the steps below to make sure that Synder has successfully synced your PayPal 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 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.
  3. 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 PayPal and QuickBooks Online data in Excel.

Step 1: Download required reports

You should already have a report from PayPal if you’ve followed the main reconciliation flow. If not, please download it by following the steps above.

We will also need a report of the PayPal clearing account from your accounting software. 

Follow this link to find the exact steps on how to generate a clearing account report in QuickBooks Online

Note: If your QuickBooks clearing account has tens of thousands of transactions, it might not download the full dataset. After downloading one of the reports above, check for data completeness. If the report is missing data, try the alternative download method.

Step 2: Prepare your Excel data for comparison

How to prepare your PayPal report

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

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

How to prepare your QuickBooks Online report

QuickBooks report also has details that you don’t need for comparison.
Copy values of Num and Amount columns into a new sheet. This will be our QuickBooks Online clean report. 

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

Step 3: Consolidate multiple lines into one entry per transaction

PayPal transactions may appear as multiple line items in QuickBooks Online (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. Click the + (plus sign) to add this reference.
  5. In the Use labels in the section, check BOTH boxes:
    1. ☑️ Top row (uses column headers);
    2. ☑️ Left column (uses IDs as grouping criteria)
  1. 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:

  • PayPal original report data
  • QuickBooks Online report data 
  • Comparison Analysis (your working sheet)

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

  • PayPal Transaction ID
  • PayPal Amount
  • QuickBooks Transaction ID
  • QuickBooks 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 PayPal and QuickBooks Online that have shared IDs. This process helps us identify any discrepancies in amounts or missing transactions within QuickBooks Online.

1. Set up your comparison formula

  1. Copy your cleaned PayPal IDs and amounts to columns A and B.
  2. In the Lookup column, use VLOOKUP to find matching QuickBooks Online amounts:

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

Where:

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

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

2. Identify discrepancies

Perfect matches should show 0 in the difference column.

Common discrepancy indicators include:

  • Negative number = QuickBooks Online amount is higher than the PayPal amount.
  • Positive number = PayPal amount is higher than the QuickBooks Online amount. 
  • N/A = Transaction ID exists in PayPal but not in QuickBooks Online.

Step 5: Address common discrepancies

1. Missing transactions in QuickBooks Online

Possible causes:

Actions to take:

  1. Check Synder’s sync logs for failed transactions.
  2. Force a manual sync in Synder for the missing period.
  3. Confirm timezone settings match between PayPal reports (PST/UTC) and Synder.

2. Amount differences

Possible causes:

  • Currency conversion differences between marketplaces
  • Partial refunds not properly matched to original orders
  • Difference in fee calculations between PayPal 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 PayPal connections in Synder.
  4. Review any manual clearing 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 PayPal and QuickBooks Online
  • Summary of your findings (e.g., “Found 5 missing fulfillment 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.
  4. Maintain timezone consistency across PayPal, 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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