The proper way to Invoice and Receive Payment for Shopify Orders

Hello there, @BiggerFishing.

Let's ensure the invoice and payment for Shopify Orders are handled properly in QuickBooks.

Yes, you're correct. It would be better to mark each invoice as paid and set it to Undeposited funds. It's a holding account that tracks all the payments you receive by cash, check, and credit card before they are deposited into your bank account. Follow these steps:

1. Select + New.
2. Select Receive Payments, then enter all the payment information.
3. Select the checkbox next to the invoice you would like the payment to be applied to.
4. Select Undeposited funds as the deposit to the account.
5. Choose Save to record the transaction.

Then, what you can do with the fee is record a bank service charge as a negative amount using the Bank Deposit feature. Here's how:

1. Go to the +New button.
2. Select Bank Deposit under Other.
3. Place a checkmark to select the payment you want to deposit under the Select Existing Payments section.
4. From the Add other funds to this deposit section, enter the amount of the bank service fee as a negative amount.
5. From the Account section, select the Expense account you usually use in tracking bank fees.
6. Make sure the amount is correct. Then, hit Save.
   

Once you get the Shopify ACH transfer downloaded from the Banking menu, you can match the existing entries. For more tips and additional information on how you can keep your transactions organize, feel free to check the articles below:
 

• Categorize and match online bank transactions in QuickBooks Online.

• Reconcile an account in QuickBooks Online.

Visit again if you have follow-up questions about handling transactions coming from a third-party merchant service. I'll be around to assist you. Take care always and have a good one!

@BiggerFishing 

Another option, consider having a 3rd party app to avoid any duplicate incomes. To reconcile your payouts can be a major time-suck. And when you're having to comb through hundreds or thousands of orders, that becomes a nightmare. You can set it once and the app can post a summary of your store sales. Your fees are split out so you can match your deposits and be done.

Thank you so much for that explanation. I have been able to create the invoice, then receive payment and have it deposit into undeposited funds.

The issue I am running into is that Quickbooks is asking me to review the transaction as well, and no option when I review to match any payments.

Let me give an example that may make my question clearer:

A customer named Bob places an order on my website for $15.00, pays credit card through shopify. I create an invoice in QB, and then immediately after I receive payment in QB for that invoice, I mark as 'shopify payment' as payment method I created, and I have funds deposit into category 'Undeposited Funds'

A few days later, Shopify transfers $14.25 to my bank(sale - fee). When I login to quickbooks, it already notices the transfer and asks me to review the transaction to log, which I can record as transfer, from undeposited funds but no option to link that payment from Bob, to mark his payment as deposited?

If I just go to new deposit and create manually I think I've got it, but the whole matching and review is confusing me thinking I may be accidentally duplicating it? 

Let me shed a light on that process, BiggerFishing.

You'll have to deposit the payment first from the Undeposited Fund account to your bank account. This way, QuickBooks will be able to show that payment when matching the downloaded transaction.

Moreover, creating a bank deposit won't generate any duplicates since you're just moving the funds to the appropriate bank account. When you're ready, here's how to do it:

1. Click the + New button.
2. Select Bank Deposit.
3. From the Account drop-down menu, choose the account you want to put the money into.
4. Tick the checkbox for the payment you want to deposit.
5. Hit Save and close, then go to the Banking menu.
6. Match the payment to the downloaded transaction.

Lastly, I recommend reading this article to speed up the reviewing process of your downloaded online banking transactions: Set up bank rules in QuickBooks Online.

Feel welcome to tag me in your comments and posts if you need more help in handling your other transactions. Have a pleasant day ahead.