Shopify Clearing Account Reconciliation Guide – Per Transaction mode

• Main Reconciliation Flow
• If your clearing account does not reconcile
• When to reach out  to support
• Best practices for ongoing reconciliation

We will help you in your Shopify clearing account reconciliation so that the balance in your accounting platform matches Shopify Payments.

This guide explains how to:

• Find out the starting and ending balance of your Shopify account.
• Reconcile your clearing account
• Compare data between Shopify 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 Shopify with Synder
• Your clearing account does not reconcile or zero out automatically
• You want to verify that Shopify and accounting records match

After completing the steps described, your Shopify clearing account reconciliation will be correct, with all sales, payouts, and fees accurately reflected in your books.

Shopify Clearing Account Reconciliation Flow

Start with the Main Reconciliation Flow below to compare Shopify Payments totals with your clearing account balance. To reconcile your Shopify clearing account, we need to gather the following information:

• Shopify Payments amounts
• QuickBooks Shopify clearing account report

To find Shopify Payments amounts, follow these steps:

1. Navigate to Analytics->Reports.
2. Find the Finance Summary report.

3. Select a time period that you want to reconcile.

4. Find the Payments group and locate Shopify Payments.
   
   Note: Add any other payment processors you’re syncing along with Shopify Payments. In this example, we are also syncing AfterPay payments with the Shopify integration, and we will include it in the calculation.
   
5. Sum both of these amounts.

Follow this link to find the exact steps on how to generate a clearing account report in QuickBooks and how to find this sum. The same logic can be applied to other accounting software like Xero and Oracle NetSuite

The amount you receive will match the sum of these transaction types in the Shopify (required for Synder) clearing account in your QuickBooks. 

Congratulations, you have successfully reconciled your Shopify! 

For some reason, the numbers don’t match. Continue reading to troubleshoot!

If your clearing account does not reconcile

When the balances between your Shopify and QuickBooks Online reports don’t match, it’s often caused by unsynchronized transactions. Follow the steps below to make sure that Synder has successfully synced your Shopify data. If even one transaction isn’t synced, your clearing account won’t reconcile.

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. These transactions prevent reconciliation.
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 your balances still don’t match after these checks, move on to Advanced Comparison (Excel Method) below to identify specific discrepancies.

Step 1: Download required reports

If you followed the previous steps, you should already have the required report from QuickBooks Online.

However, you still need to download a report from Shopify. Here’s how you can do that:

1. Navigate to Analytics->Reports.
2. Find Net payments by gateway report.

3. Select your reconciliation date.
4. Click Export and export again.

Step 2: Prepare your Excel data for comparison

How to prepare your Shopify report

Shopify report includes a lot of transaction details that you don’t need for comparison. Remove them by following these steps: 

1. Apply a filter to the whole upper row (highlighted in blue on the screenshot below).
2. Filter only CAPTURE, SALE and types in the Kind column.
3. Filter only SUCCESS types in the Status column.

4. Copy values of order_id and shop_amount columns into a new sheet. This will be our Shopify clean report. 

IMPORTANT: The Shopify report shows refunds as positive amounts. To match the QuickBooks format, which displays refunds as negative values, please convert the positive Shopify refund amounts to negatives.

Now your report should look similar to the one below.

How to prepare your QuickBooks Online report

QuickBooks report also has details that you don’t need. Here’s how to remove them:

1. Filter only Payment, Refund and Sales Receipt in the Transaction Type column. Payouts and fees will not be necessary for the comparison

2. Memo Description contains Shopify transaction ID. To remove unwanted text, we can use an Excel formula:

1. Create a new column called “Clean ID.”
2. Copy and paste the formula below:
   
   =MID(E2, SEARCH(“orderid_”, E2) + 8, 13) 

Where: 

E2 is the column+row to search.
SEARCH(“orderid_”, E2)  Finds the starting position of “orderid_”
+8 amount of characters the search should skip.
13 the number of characters ID consists of.

3. Apply this formula to the whole Clean ID column. 
4. Copy values of the Clean ID and Amount columns into a new sheet. This will be our Shopify clean report. 

Now your report should look similar to the one below.

Step 3: Consolidate multiple lines into one entry per transaction

Shopify 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. Here’s how it should look:

Perform the same steps for your Shopify report.

Step 4: Organize your data

1. Create a new sheet for your Comparison Analysis.
2. In your Comparison Analysis sheet, create columns for:

• Shopify Transaction ID. 
• Shopify Amount
  Copy and paste columns from your Clean Shopify report.
• QuickBooks Transaction ID
• QuickBooks Transaction Amount
  Copy and paste columns from your Clean QuickBooks report.
• Lookup
• Difference

Here’s how the end result should look:

Step 5: Compare data using VLOOKUP

Our objective is to match transaction amounts from Shopify 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 Shopify 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 = Shopify 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 Shopify amount.

2. Identify discrepancies. 

Note: Perfect matches should show 0 in the difference column.

Common discrepancy indicators include:

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

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

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 Shopify 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 Shopify 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 Shopify connections in Synder.
4. Review any manual clearing account adjustments.

When to reach out  to support

Please 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 Shopify 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 Shopify, 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 the Synder Team via online support chat or email with any questions you have – we are always happy to help you!