How to Receive Payments in QuickBooks Online

Getting paid on time is essential for any business. However, if you manage payments manually, it can take time and create errors. With QuickBooks Online, you can simplify the entire process of receive payments in QuickBooks Online from sending invoices to receiving and recording payments, all in one place.

QuickBooks Online allows you to accept payments through multiple methods, such as credit cards, bank transfers, and online payment links. It also automatically updates your records, reduces manual work, and helps you track every transaction with ease.

In this guide, you’ll learn how to set up payments, record customer transactions, manage deposits, and avoid common mistakes. So, you can get paid with ease and keep your accounts accurate.

Does Your Business Qualify for QuickBooks Payments?

However, QuickBooks Online works for most businesses; its QuickBooks Payments feature has specific requirements to ensure security and compliance. Before you start accepting online payments, you need to confirm that your business meets these conditions.

Eligibility Requirements and How to Check

Before you can use the “Pay Now” option on your invoices in QuickBooks Online, your business needs to meet some basic requirements:

• Primary Admin Access: Only the Primary Admin can apply for QuickBooks Payments. Other users don’t have permission to set it up.
• Verified Business Details: You need to provide a valid U.S. tax ID (SSN or EIN) and a real business address for identity verification.
• Allowed Industry: Some high-risk industries (like CBD or similar businesses) are not supported.
• Approval Process: Your application will be reviewed and may include a credit check. Approval usually takes 1–3 business days.
• Bank Account Required: You must connect a valid U.S. bank account to receive payments. You can also use a QuickBooks Checking account for faster deposits.

How to Check Your Eligibility Status

You can quickly check if you’re ready to apply directly within your account:

• Select the Settings in the top right corner.
• Choose Account and Settings.
• Go to the Payments tab on the left menu.
• If you see a “Learn more” or “Set up” button, you are eligible to start the application process. If you already have an account, you will see a “Connect” option instead.

Setting Up QuickBooks Online to Receive Payments

Once your business is eligible, the next step is to set up how you want to receive payments in QuickBooks Online. This is a one-time setup that connects your payment methods, bank account, and invoices so you can get paid easily and without delays.

Configure QuickBooks Payment Preferences

Before sending invoices, you should set your payment preferences properly:

• Go to Settings >> Account and Settings>>Payments.
• Enable Payment Methods like:
  • Credit/Debit Cards
  • Bank Transfers (ACH) (usually lower fees)
• Choose your Deposit Speed:
  • Standard (1–3 business days)
  • Instant (extra fee may apply)
• Set a default Invoice Message with payment terms (e.g., “Due on receipt”)
• Enable automatic matching to Connect Bank Deposits with invoices

These settings help automate your payment process and reduce manual work.

Create and Send Invoices to Customers

After setup, you can start sending invoices and receiving payments:

• Click + New >> Invoice.
• Select a customer and add products/services.
• QuickBooks will calculate the total automatically (including taxes).
• Enable online payment options (Cards / Bank Transfer).
• Click Save and Send.

The customer will receive an email with a “Pay Now” button.  Once they pay, QuickBooks automatically updates the invoice status as Paid or Payment Pending, and you’ll get a notification.

How to Record and Receive Customer Payments in QuickBooks Online

Recording payments correctly in QuickBooks Online helps keep your records accurate. Customers may pay in full, partially, or for multiple invoices, and QuickBooks makes it easy to record payments in QuickBooks Online without confusion.

Recording Payment for a Single Invoice

When a customer pays one invoice in full:

• Go to + New>>Receive Payment.
• Select the customer name.
• Choose the invoice from outstanding transactions.
• Make sure the amount received matches the invoice
• Select payment method (cash, check, etc.)
• Choose Deposit to (usually Undeposited Funds).
• Click Save and Close.

The invoice will be marked as Paid.

Recording a Partial Payment for an Invoice

If a customer pays only part of the amount:

• Go to + New>> Receive Payment.
• Select the customer and invoice.
• Enter the actual amount received (less than total).
• At last, save the payment.

QuickBooks will mark the invoice as Partial and show the remaining balance.

Applying a Payment to Multiple Invoices

If one payment covers multiple invoices:

• Open Receive Payment.
• After that, select the customer.
• Check all relevant invoices.
• Enter the total payment amount.
• Adjust amounts if needed.
• At last, click on the Save button. 

QuickBooks will automatically apply the payment to the selected invoices.

Taking Online Payments Through QuickBooks

With QuickBooks Payments enabled, you can automate the process:

• Send Invoices with online payment options enabled.
• Customer clicks the “Pay Now” button.
• They pay using a Card or a Bank transfer.

Once payment is made, QuickBooks automatically:

• Marks the Invoice as Paid.
• Records the Transaction.
• Matches it with your bank deposit.

This saves time and reduces manual work.

How Long Does It Take to Receive Payments in QuickBooks Online?

In QuickBooks Online, the time you receive payments depends on the method used and your account setup. Here’s what you can expect:

• Credit Cards & Digital Wallets: Usually take 1–2 business days.
• ACH Bank Transfers: Generally, it takes 2–5 business days (new accounts may have up to a 5-day hold initially).
• Instant Deposit: Funds can arrive within minutes (an around 1.75% fee may apply).
• QuickBooks Checking: Eligible users may get free instant deposits.

Note: Payments made after 3:00 PM PT, or on weekends and holidays, are processed on the next business day.

Payment Options in QuickBooks Online

QuickBooks Online gives you multiple ways to receive payments. Hence, it becomes easy for customers to pay you and helps you manage your cash flow better. You can choose the option that best fits your business needs.

QuickBooks Instant Payments

If you don’t want to wait for standard deposits:

• Get funds within minutes (24/7).
• Available for eligible payments.
• Costs around 1.75% per transaction.
• Option available in the Sales or Deposits tab.

Useful when you need quick access to money.

Late Payments: How to Manage and Follow Up

QuickBooks helps you handle overdue payments efficiently:

• Set up automatic payment reminders (e.g., 3, 7, or 14 days after due date).
• Add late fees (fixed amount or percentage).
• Send customer statements showing all unpaid invoices.

These features help you follow up professionally and get paid faster.

You can also receive payments using the mobile app:

• Create and send invoices instantly on the go.
• Accept payments from anywhere.
• Deposit checks using your phone camera.
• Allow payments via QR codes (card, Apple Pay, Google Pay).

This is perfect for businesses that need flexibility outside the office.

Managing Undeposited Funds and Depositing Payments to Your Bank

When you receive payments in QuickBooks Online, some payments are first stored in Undeposited Funds. In QuickBooks Online, the Undeposited Funds account, also called Payments to Deposit, works like a temporary holding place for your payments before they are deposited into your bank. Using this feature correctly helps ensure your QuickBooks records match your actual bank statement.

How to Review and Clear the Undeposited Funds Account

To move your payments from Undeposited Funds to your bank account, follow these steps:

• Click + New >>Bank Deposit.
• Select your bank account in the Account field.
• After that. Enter the deposit date.
• Review the list of payments in Undeposited Funds.
• Check the payments you want to include in the deposit.
• Make sure the total matches your actual bank deposit slip.
• Lastly, click Save and Close.

Once saved, the selected payments are moved from Undeposited Funds to your bank account in QuickBooks.

Tip: If you deposit multiple checks together, select all of them in one deposit. It creates a single entry that matches your bank statement and makes reconciliation much easier.

Top Benefits of Using QuickBooks to Receive Customer Payments

Using QuickBooks Online for payments helps you manage everything in one place. It connects your payment process with your accounting. It makes your work fast and accurate.

Some of the Key Advantages for Small Businesses

• Fast Payments: Adding a “Pay Now” button lets customers pay instantly via card, bank transfer, or digital wallets. It helps you get paid quickly.
• Automatic Bookkeeping: Payments are recorded automatically, invoices are marked as Paid, and deposits are matched with your bank.
• Better Cash Flow Visibility: You get real-time updates when customers view or pay invoices, helping you track your finances easily. 
• Fewer Errors: Automation reduces manual work and minimizes the chances of mistakes.
• Mobile Flexibility: You can accept payments anytime using the mobile app, even outside the office.
• Secure Transactions: QuickBooks offers strong security, encryption, and protection against fraud and chargebacks.

Troubleshooting Payment Issues in QuickBooks Online

Even when using QuickBooks Online, payment issues can sometimes happen. Knowing how to identify and fix these problems helps keep your records accurate and makes bank reconciliation easier.

Common Errors When Payments Are Not Recorded Correctly

Most payment issues happen due to small mistakes in the process:

• Duplicate Entries: Happens when you record a payment manually and also add it again from the bank feed. Always use Match instead of Add.
• Payments in Undeposited Funds: If payment shows as paid but not in the bank, it is still in Undeposited Funds and needs a bank deposit.
• Unapplied Payments: Payment is recorded but not linked to an invoice, leaving the invoice open.
• Wrong Deposit Account: Selecting the wrong bank account can cause mismatched balances.

How to Prevent Invoice and Payment Mistakes

You can avoid most issues by following simple practices:

• Use the Match Feature: Always check the bank feed and match transactions instead of adding duplicates.
• Follow a Consistent Method: Use either Undeposited Funds or direct deposit, not both randomly.
• Check Open Invoices Regularly: Review unpaid invoices weekly to catch errors early.
• Enable Auto-Apply Credits: Turn on this setting so extra payments are applied automatically.

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Frequently Asked Questions