Summary Sync: Stripe Clearing Account Reconciliation Guide for Synder Users

Overview

Synder syncs sales, refunds, payouts, and fees from Stripe. Depending on your configuration, transactions are recorded in your accounting platform as summarized journal entries.

This guide explains how to:

  • Identify the starting and ending balance of your Stripe account
  • Reconcile your clearing account
  • Compare Stripe and accounting data to identify discrepancies

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

Use this guide if:

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

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

Main reconciliation flow

To reconcile your Stripe clearing account, we need to figure out the starting and ending balances in your Stripe account. Knowing your starting and ending balances gives you a clear reference point for matching your QuickBooks Online accounts. Stripe provides simple access to both balances on their reports page:

  1. Visit the reports page.
  2. Go to the ‘Balances’ tab.
  3. Select the date range you are reconciling.

It will show you both the starting and the ending balances of your Stripe account:

Starting balance

If you have been using Stripe before Synder, please ensure that your Stripe starting balance matches the opening balance of your Stripe(required by Synder) clearing account. 

For example, if you began using Synder on October 1, your Stripe clearing account balance in Synder would be $0, while the actual balance in Stripe is different. Using the example above, the Stripe starting balance on October 1 is $22,193.10, so the opening balance for the Stripe clearing account in Synder should also be $22,193.10. 

After syncing all transactions, the ending balance in Stripe will match the balance in your Stripe clearing account.

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 Stripe clearing account for the reconciled month.

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

Congratulations!

The amounts you will see in the Synder Balance sheet report will match your Stripe balance, meaning the reconciliation was successful.

If your clearing account does not reconcile

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

Step 1: Download required reports

Here’s how you can download a Balance change from activity report inStripe:

  1. Log into your Stripe Dashboard.
  2. Navigate to Reports → Balance Summary.
  1. Set your date range for the reconciliation period.
  2. Select the “Balance change from activity” report.
  1. Important: When downloading, ensure you include all 54 columns.

We will also need a report of the Stripe 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 Online 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 Stripe report

Stripe report includes a lot of transaction details that you don’t need for comparison.
You need the balance_transaction and net columns.
The balance_transaction column contains IDs that need to be cleaned for easier matching. You can use the following formula to extract the clean ID:
=MID(A2, 8, 13)

Where:

  • A2 =  the cell containing the original ID

Here’s how the end result should look like.



Copy values of Purified ID and total columns into a new sheet. This will be our Stripe clean report.

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

How to prepare your QuickBooks Online report

The QuickBooks Online report also contains details that aren’t needed for comparison. You only need the Num and 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.

The num column contains IDs that need to be cleaned for easier matching. You can use the following formula to extract the clean ID:
=LEFT(C3, 13)

Where:

  • C3 =  the cell containing the original ID

Here’s how the end result should look like.

Copy values of Purified ID and Amountcolumns into a new sheet. This will be our Stripe clean report.

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

Step 3: Consolidate multiple lines into one entry per transaction

Stripe 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)
  6. 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:

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

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

  • Stripe Transaction ID
  • Stripe Amount
  • QuickBooks Online Transaction ID
  • QuickBooks Online 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 Stripe 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 Stripe IDs and amounts to columns A and B.
  2. In the Lookup column, use VLOOKUP to find matching QuickBooks Online amounts:

=VLOOKUP(A3,C:D,2,FALSE)

Where:

  • A3 = Stripe 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 Stripe 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 Stripe amount.
  • Positive number = Stripe amount is higher than the QuickBooks Online amount. 
  • N/A = Transaction ID exists in Stripe but not in QuickBooks Online.

Step 6: 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 Stripe 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 Stripe 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 Stripe 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 Stripe 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 Stripe, 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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