When you sell through Shopify, the payment for orders would be taken by Shopify and Shopify will deposit the payments to you (usually daily) but the payment paid to you would be less than your total sales amount. The differences are due to Shopify's fees on payment, any chargeback on past orders, refunds, or any holds on payments. It is important for you to classify the differences and book them correctly and usually as expenses.
We recommend creating a separate GL account (let's call it Shopify Payment) to record payments received from Shopify. This way, online payment is isolated from the rest of your payments which might come from different sources
This new account is the account you will reconcile with the deposits coming from Shopify into your bank account . You would reconcile and clear the balance in this account and deposit into the actual bank account .
To change the account used to record payments for Shopify orders, you would go into tools menu, webstores and setting and find setting under Settings For Payments.
Let's look at an example.
Assuming you are reconciling weekly. The steps to reconcile would start by first looking at the balance of this account "Shopify payment" . It holds the total sales amount for shopify(excluding any deductions).
You would then look at the payout record for Shopify for the week. The total will be smaller than the balance of the Shopify payment account. The difference is what you need to reconcile. They usually consists of fee deductions, chargebacks, refunds, holdbacks. You would record a single GL entry to move the money from Shopify payment to your bank account once you determine what the difference is.
Let's say the deposit from Shopify is 90 dollar and the balance in your Shopify Payment account is 100. You determine the 10 dollar difference to be an expense due to feeds . The GL entry would look like this
Shopify Payment 100
Bank Account 90
Shopify Fee Expense 10
After this, the balance in Shopify Payment account is zero and you would repeat this for your next reconciliation.