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Understanding customer payments in QuickBooks Online

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Keeping track of customer payments is an important part of managing your business. Maybe a customer says they've paid an invoice, but it's still showing as unpaid. Or maybe you've recorded a payment in QuickBooks, but can't find the money in your bank account. QuickBooks has several ways to help you track payments, check outstanding balances and understand where your money is.

In this mini guide, we'll walk through some common customer payment questions, what to check and where to find help if something doesn't look right.

The steps below mainly apply to QuickBooks Online. Some features and options may differ depending on your subscription and the payment service you're using.

1. How can I check if a customer has paid?

If you're unsure whether a customer has paid an invoice, the first place to check is the invoice status in QuickBooks.

Here's what to do:

Go to Sales & Get Paid and select Invoices. Depending on your QuickBooks layout, you may see Get paid > Invoices instead.
Find the invoice you want to check.
Look at the Status column to see where things stand.
Select the invoice to review its details and any payments recorded against it.

You might see statuses such as:

Sent: The invoice has been emailed to your customer.
Viewed: Your customer has opened the invoice.
Partially paid: A payment has been recorded, but there's still an outstanding balance.
Paid: The invoice has been paid in full.
Overdue: The payment due date has passed and there's still an outstanding balance.

Remember, an invoice showing as paid in QuickBooks doesn't always mean the money has reached your bank account yet. If you're using a payment processing service, the funds may still be settling.

Helpful guide: View sales transactions in QuickBooks Online

2. How do I record a customer payment?

If a customer has paid you by bank transfer, cash or another method outside QuickBooks, you'll need to make sure the payment is recorded against the correct invoice.

This helps keep your customer balances accurate and prevents invoices from continuing to appear as unpaid.

Here's how to record a payment:

Select + New or + Create.
Choose Receive payment.
Select the customer from the dropdown menu.
Choose the payment method.
In Deposit to, select the account where the payment should be recorded.
Under Outstanding Transactions, select the invoice the payment relates to.
Check the payment amount and select Save and close.

If the customer has paid the full amount, the invoice should no longer show an outstanding balance.

A quick tip: If you've already recorded the payment in QuickBooks and it appears in your connected bank feed, look for an option to match the bank transaction to the existing payment rather than recording it again. This helps avoid duplicate transactions.

Helpful guide: Record invoice payments in QuickBooks

3. My customer has paid, but I can't find the deposit

This is a common question, especially when a payment has been recorded in QuickBooks but doesn't appear where you expected.

There are a few things worth checking before assuming the payment is missing.

Check where the payment was recorded

When you record a payment, QuickBooks asks where the money should be deposited.

If you selected Undeposited Funds, the payment is being held in a temporary account within QuickBooks until it's included in a bank deposit.

To review the payment:

Go to Sales & Get Paid, then Sales transactions.
Find the payment you're looking for.
Open the transaction and check the Deposit to field.
If appropriate, check whether the payment is sitting in Undeposited Funds or has already been included in a bank deposit.

Check your bank transactions

If your bank account is connected to QuickBooks, go to Accounting > Bank transactions and look for the payment.

Keep in mind that several customer payments might appear as one combined deposit in your bank account, particularly if they've been grouped together or processed through a payment provider.

If you're using QuickBooks Payments and the invoice shows as paid but the funds haven't arrived, the payment may still be settling. Check your payment status, bank details and any emails from QuickBooks before contacting Support.

Helpful guides:

4. What if a customer only pays part of an invoice?

Sometimes a customer might pay an invoice in instalments or send less than the full amount owed.

You don't need to create a new invoice each time this happens. QuickBooks allows you to record partial payments against an existing invoice.

Here's how:

Select + New or + Create, then Receive payment.
Select the customer.
Choose the payment method and deposit account.
In Amount received, enter the amount the customer actually paid.
Select the invoice the payment relates to.
Select Save and close.

QuickBooks will keep track of the remaining balance, so you can see how much the customer still owes.

For example, if you send an invoice for £500 and your customer pays £200, QuickBooks can record the £200 payment while leaving £300 outstanding.

When the customer pays the remaining amount, you can record another payment against the same invoice.

Helpful guide: Record full and partial invoice payments

5. How do I refund a customer?

There may be times when you need to return money to a customer, whether they've returned an item, cancelled a service or accidentally overpaid.

The important thing is to record the refund correctly so your customer balance and accounting records remain accurate.

The process depends on why you're issuing the refund.

Refunding an item or service: You can generally use a refund receipt to record the refund.
Refunding a previously paid invoice: Some situations require a credit note and an expense to record and link the refund correctly.
Refunding an overpayment: You'll need to account for the customer's existing credit and link the refund to it.

If you're using QuickBooks Payments, check the relevant refund instructions for your payment method before processing anything.

It's worth taking a moment to identify the correct refund process rather than deleting the original payment, as this could affect your records.

Helpful guides:

A few tips for keeping customer payments organised

Keeping on top of your payments can make it easier to spot issues before they become bigger problems.

It's worth regularly checking that:

Customer payments have been recorded against the correct invoices.
Partially paid invoices show the correct outstanding balances.
Payments in your bank feed are matched to existing QuickBooks transactions where appropriate.
Deposits recorded in QuickBooks match the amounts received in your bank account.
Refunds and customer credits have been recorded correctly.

You can also use the Sales transactions page to review invoices, payments and other customer transactions in one place.

Helpful guide: Match your bank and credit card transactions

Need a hand with a customer payment?

If something isn't adding up, feel free to start a discussion here in the Community.

Let us know what you're trying to do, whether you're recording a payment, tracking a deposit or dealing with a refund, and where you're getting stuck.

Just remember not to share customer bank details, card information or other sensitive payment information in a public Community post.