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How to record credit card processing fee properly.
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"Assuming credit card fees are an expense account on the P&L, and you are entering these expenses as negatives, won't it mess up financials?"
Entering as Negative in the Deposit = shows you incurred an Expense.
For those of you familiar with Debits-Credits:
The Deposit to banking is a Debit
The details are Credits
Checks against Checking are Credits
The details here are Debits, such as Debit Banking Fee
So, putting a Negative Detail into your Deposit screen = just created a Debit to that Banking Fee Expense account.
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Everyone of the desktop products allow multiple line items in a deposit. Other than the deposit option you setup a bank type account in your chart of accounts for credid card payments. Make your deposits here, write checks from this account for the processing fees, and transfer funds from this account to your bank account when funding status is known.
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I'm having the same issue/question with qb online. I cannot see a record deposits screen (after I record an online sale as a sales receipt). We've been doing them as invoices so that we can enter the credit card fee expense. Trying to find a new way, and I can't make these suggestions work with qb online.

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Thanks for joining the conversation, freshwatersensations,
I can help you record your credit card fee expense in QuickBooks Online.
There's just a few steps we need to do to get you all set! Lets say you have a $50 invoice and a $2 credit card fee, which gives you a $48 net bank deposit.
Step 1: Create the customer invoice.
- Click the Plus (+) icon.
- Select Invoice.
- Enter the exact amount to be invoiced. (See screenshot below)
Step 2: Receive the payment.
- On the invoice, click the Receive Payment button.
- Select the correct invoice on the Receive Payment screen.
- In the Deposit to field, choose Undeposited Funds.
- Click Save and close. (See screenshot attached)
Step 3: Enter a Bank Deposit for the fee to relieve the balance from Undeposited Funds account to bank account. (See screenshot)
- Click the QuickBooks Plus (+) icon.
- Select Bank Deposit.
- Mark the invoice payment you received previously from the Select the payments included in this deposit section.
- Expand the Add funds to this deposit section to add a new line item.
- In the Received From column, enter the credit card fee as a vendor.
- In the Account column, add an expense account for the fee.
- In the Amount field, enter a negative fee amount.
- Make sure the deposit matches the net bank deposit amount.
- Click Save and close.
That should get you on the right track, freshwatersensations. Please let me know if you need further assistance with recording the credit card fee. I'll be available to help you anytime. Have a great day!

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I'm jumping in here too, same problem with QBO. in step 2, i can't save with out a value entered. you have 0 in your screen shot. what am i doing wrong?
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Hi iamluvinlife,
I'm actually seeing 50.00 on the screenshot in Step 2: Receive the Payment. The amount is the same as the invoice.
When you pay your invoice, pay it in full. Then, only deduct the credit card fees when you deposit the payment, like how Jen_D do it in her screenshot in Step 3. Please do not enter zero, you'll get an error if you do that.
Let us know if you have other questions.
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Perfect thank you

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HI
I am having this issue as well in QBO
in your step 3 Bank Deposit, I cannot see Select the payments included in this deposit
Please help.
Thanks
Samara
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Hello Samipami,
The Select the payments included in this deposit section will only appear if you have created sales transactions (sales receipts or invoice payments) that are deposited to Undeposited Funds.
It's possible that the invoice payment was deposited directly to the bank account. You can review the Deposit to field of the invoice payments.
Let us know if you need anything else. We got your back!
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Thank you! This is freshwatersensations under a different username. One question, the account to which I'm depositing (negative) funds...you list a "Credit Card Fees (Expense Account)." I'm not sure which account I should choose. Do I have to list an account? Does this mean expense CATEGORY? It all comes out of the business, and we use reports to break down the expenses by category.
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Expense account is a Type; Category is some sort of additional cross-reference.
Example:
My total sales in UF to select is $5,000 but I see I incurred a $10 Wire Fee for a payment to me made electronically. In reality, my Bank Deposit was $4,990. That means I select the $5,000 of customer payments and I enter the Negative $10 as Bank Fee Expense to me. The reason I Lost that amount, is the Expense account I put it against.
Net deposit = $4,990 "Net" = The Math.