A2X generates a summary entry for each payment gateway connected to your Shopify store. While Shopify Payments deposits typically match your bank account directly, third-party processors require a clearing account.
This allows you to accurately track your sales, manage timing differences, and account for processing fees.
Before You Start
You must set up your clearing accounts as Current Asset accounts in your accounting system.
We highly recommend creating a separate, dedicated clearing account for each payment gateway you use (e.g., "Klarna Clearing," "PayPal Clearing"). This prevents commingled funds and makes monthly reconciliations much easier.
Why do I need a clearing account?
A payment clearing account tracks undeposited funds or funds in transit from your payment provider to your checking account. It acts as a temporary holding account.
You need a clearing account for third-party gateways for two main reasons:
Hidden Fees: Most payment providers deduct their processing fees before depositing funds into your bank account. Because Shopify or A2X cannot see this fee deduction, the payout amount in A2X will not perfectly match your bank deposit.
Timing Differences: There is often a delay between the date funds are collected from the buyer and the date they are deposited into your checking account.
Note: For transactions processed directly via Shopify Payments, A2X summaries will match your checking account deposits exactly. You generally do not need a clearing account for Shopify Payments.
How A2X processes gateway payouts
A2X brings in each payout from your different payment gateways separately. It creates a detailed entry that breaks out all of the different transaction types, like sales, refunds, shipping, and taxes.
To balance this entry, A2X includes an offset entry line mapped directly to your payment gateway clearing account.
Steps to reconcile your clearing accounts
Follow these three steps to keep your clearing accounts balanced and account for any missing fees.
⚠️ Warning: The reconciliation process below is a general guide. Please consult your financial advisor or accountant to ensure you have the correct mappings and processes for your specific business.
1. Post the A2X payout entry
Review your payout in A2X and post it to your accounting system. This action records your sales, taxes, and shipping, and debits the total payout amount to your designated clearing account.
2. Categorize your bank deposits
When the actual funds from the payment gateway clear your checking account, categorize those deposits in your accounting system to the same corresponding clearing account. This credits the clearing account, reducing its balance.
3. Account for processing fees and adjustments
Because the payment gateway deducted fees before sending you the deposit, your clearing account will likely still have a balance. Generate a monthly statement from your payment processor (e.g., Klarna or PayPal) to identify these fees.
Create a manual journal entry in your accounting system to expense these processing fees, which will credit the clearing account and reduce the balance.
This is also the time to record any disputes or chargebacks processed directly through the payment platform. These transactions occur outside the Shopify sales channel integration and will not appear in your A2X entries, so they must be recorded manually against the clearing account.
Note: If there is still a small balance left in the clearing account at month-end after recording fees, this generally represents "funds in transit" that have not yet cleared your checking account.
Hyperthetic Example
Suppose A2X posts a Stripe payout entry of $6,519.49 to your Stripe Clearing account (Step 1). When Stripe deposits $5,456.80 into your checking account and you categorize it to the clearing account (Step 2), the remaining balance is $1,062.69. You then check your Stripe monthly statement and find $500.00 in processing fees. After recording a journal entry for these fees (Step 3), the clearing account balance is $562.69, representing funds still in transit to your checking account.
Troubleshooting
My clearing account balance keeps growing Verify that you are categorizing your bank deposits to the clearing account, not to a sales account. Ensure you are also manually logging your processor fees each month.
I have chargebacks or disputes Chargebacks processed directly through the payment platform occur outside of the Shopify sales channel integration. You will need to record these manually in your accounting system against the clearing account.
Missing payment gateway payouts Verify that your Shopify integration is actively syncing and that the payment gateway has processed the funds on their end.
FAQs
Do I need a clearing account for Shopify Payments? No. A2X summaries for Shopify Payments will match your checking account deposits, meaning you can reconcile them directly without a clearing account.
Can A2X automatically post my third-party gateway fees? No. Because payment gateways deduct their fees before sending the payout data to Shopify, A2X cannot see the exact fee amount. You must use the clearing account method to calculate and manually post these fees.