Per Transaction Mode: Stripe – QuickBooks Clearing Reconciliation Guide for Synder Users

Understanding how Synder works with Clearing Accounts

What is a clearing account? It’s a temporary holding account that Synder uses to accurately track your payment platform transactions before they settle into your bank account. When Stripe processes payments, fees, and refunds, Synder records these in your QuickBooks Online clearing account to maintain accurate financial records. Then Stripe sends the settlement payout to the bank, and Synder transfers the corresponding amount from the clearing to the checking account.

Why clearing accounts matter:

• Sales increase the clearing account balance (money coming in)
• Fees and refunds decrease the clearing account balance (money going out)
• Payouts transfer money from the clearing account to your bank account
• The clearing account balance should match your Stripe balance at any given time

We suggest reconciling this account monthly when using Synder. 

Discrepancies in Reconciliation

If your Stripe totals don’t match what you see in QuickBooks Online, it usually means that there’s a mismatch in the data being compared or some records didn’t sync properly. This guide will walk you through how to compare Stripe and QuickBooks Online reports, locate where discrepancies are coming from, and what steps to take to resolve them using Excel.

Understanding and resolving discrepancies early helps prevent accounting errors and ensures your books are audit-ready.

Starting and ending balances

Knowing your starting and ending balances gives you a clear reference point for matching your QuickBooks Online accounts. Luckily, Stripe provides simple access to both balances on their reports page:

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

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

Step 1: Checking the basics

1. Go to Synder and filter transactions by status. Make sure that all the transactions within your reconciliation period are marked as  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 these transactions are present,  your books will not reconcile.
2. Make sure you are comparing the right numbers (sales might not equal cash, for example). So, make sure you have the right numbers for reconciliation.
3. If your platform was disconnected within the reconciliation period, make sure you run “Historical Import” on the Platform transactions page to import any missing transactions.

If you’ve checked all the basics and the discrepancy still persists, download the report from Amazon and compare it with the QuickBooks report.  This will pinpoint the transactions causing the differences.

Step 2: Download required reports

From Stripe:

1. Log into your Stripe Dashboard.
2. Navigate to Reports → Balance Summary.

3. Set your date range for the reconciliation period.
4. Select the “Balance change from activity” report.

5. Important: When downloading, ensure you include all 54 columns.

From QuickBooks Online:

Method 1 – Transaction List (Recommended):

1. In QuickBooks Online, go to the Chart of Accounts.
2. Find your Stripe clearing account(s).
   • Note: You may have multiple clearing accounts if you process different currencies.
3. Click on the clearing account name.
4. Click “Run Report.”
5. Set the same date range as your Stripe report.
6. Export to Excel.

Method 2 – Balance Sheet:

1. Go to Reports → Balance Sheet.
2. Set display columns to “by month.”
3. Click on the clearing account balance for your target month.
4. Export the detailed transactions.

Step 3: Prepare your Excel data for comparison

Clean up transaction IDs

Both reports may have transaction IDs with extra text that needs to be standardized.

Common ID formats:

• Stripe: ch_1234567890abcdef
• QuickBooks Online: ch_1234567890abcdef (Customer Name) or Stripe: ch_1234567890abcdef

Update the IDs in Excel to match the formatting on both platform reports:

Use the Replace function or Find & Replace to remove extra text.

Alternatively, we can do it with formulas in Excel:

1. Create a new column called “Clean ID.”
2. Stripe ID format is not fixed—it can vary, so many formulas may work for this separation:
   

1. Apply this to both the Stripe and QuickBooks Online ID columns if needed.

Organize your data

Create separate worksheets for:

• Stripe raw data (original download)
• QuickBooks Online raw data (original download)
• Comparison analysis (your working sheet)

In your comparison analysis sheet, create columns for:

• Stripe ID (cleaned)
• Stripe Amount 
• QuickBooks Online ID (cleaned)
• QuickBooks Online Amount
• Lookup
• Difference

Step 4: 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.

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:

Excel

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

Where:

• A2 = Stripe ID you’re looking up
• C:D = Your QuickBooks Online data range (ID in column C, amount in column D)
• 2 = Return column for QuickBooks Online amount
• FALSE = Exact match only

3. In the ‘Difference’ column, calculate the difference by subtracting the looked-up amount from the Stripe amount:

Identify discrepancies

Perfect matches should show 0 in the Difference column.

Common discrepancy indicators:

• 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 is missing  on one of the platforms

Step 4: Analyze transaction types

Different Stripe transactions sync to QuickBooks Online as different record types:

Filter and compare by transaction type:

Sort your data by transaction type and review each category separately (e.g., sales vs. sales, fees vs. fees). This makes it easier to spot patterns in missing or incorrect data.

Step 5: Address common discrepancies

Missing transactions in QuickBooks Online

Possible causes:

• The transaction failed to sync due to network issues.
• The transaction was filtered out by Synder settings.
• The transaction occurred outside the sync timeframe.
• The transaction type is not supported.

Actions to take:

1. Check Synder’s sync logs for failed transactions.
2. Verify date ranges match between reports.
3. Force a manual sync in Synder for the missing period.
4. Check if transactions have a  “Pending” status.

Amount differences

Possible causes:

• The amounts differ due to currency conversion.
• Partial refunds were not properly matched.
• Fee calculations vary between the platforms,
• There are rounding differences.

Actions to take:

1. Check if the transaction involves currency conversion.
2. Verify that the transaction hasn’t been partially refunded.
3. Compare gross vs. net amounts.
4. Look for related adjustment entries.

Extra transactions in QuickBooks Online

Possible causes:

• Manual entries were created by your team,
• Transactions were synced more than once.
• Some transactions came from other payment platforms.
• Journal entries or adjustments were made.

Actions to take:

1. Look for transactions without Stripe IDs in the description,
2. Check if the description indicates manual entry.
3. Verify the transaction source in QuickBooks Online.
4. Check for duplicate processing.

Step 6: Verify your clearing account balance

After resolving individual transaction discrepancies:

1. Calculate total differences by transaction type.
2. Compare the final clearing account balance to the Stripe ending balance for the period.
3. Account for timing differences (Stripe reports by transaction date, QuickBooks Online by sync date).
4. Verify that all payouts are properly recorded as transfers to your bank account.

Step 7: When to reach out to support

Turn to support when you’ve identified specific transactions causing issues but cannot resolve them:

What to include in your support request:

• Reconciliation period (start and end dates)
• Specific transaction IDs that are causing discrepancies
• Screenshots of the problem transactions in both Stripe and QuickBooks Online
• Summary of your findings (e.g., “Found 3 missing refunds totaling $150”)
• Steps already taken to resolve the issue

Best practices for ongoing reconciliation

Following these best practices will help you catch issues early, keep your clearing account accurate, and ensure your financials stay audit-ready.

1. Reconcile monthly rather than waiting for quarter-end
2. Check your clearing account balance regularly in QuickBooks Online
3. Set up alerts in Synder for failed sync transactions
4. Maintain consistent timezone settings across Stripe, Synder, and QuickBooks Online
5. Document any manual entries made to clearing accounts
6. Keep your integration settings updated when you change Stripe configurations

If this feels a bit too complex, we can help. Book a call to explore the Pro plan—your account manager can handle it all for you.

If this sounds like a lot to manage, consider moving to Pro, and your account manager will be able to handle it from here. Book a call to see if it’s a good fit.