Applying & Recording Payments
Overview
You've received a payment — congratulations. Now it's time to record that payment in Quicken Business & Personal to keep your books accurate and your business running smoothly.
Why Recording Payments Matters
Some business owners assume that once the money hits the bank, their work is done. But to truly understand your business performance, you need to track who paid, how much, and which invoice the payment applies to.
Recording payments to invoices helps you:
✅ Keep income records accurate
✅ Avoid cash flow surprises
✅ Know what's been paid — and what's still owed
✅ Stay ready for tax time
✅ Improve your chances of getting loans or credit
✅ Save time by avoiding costly errors
💡 Good records give you insights — and insights build confidence.
🔍 What’s Your Situation?
In Quicken Business & Personal, there are four main ways to apply a payment to an invoice. How you record a payment depends on how the funds were received or deposited.
1️⃣ The payment has already been deposited and appears in your bank feed
→ Use: Link a Bank Transaction to an Invoice
Common scenarios:
Online payments (Stripe, PayPal, Square)
ACH transfers and wire transfers
Venmo, Zelle, or other digital payments
Mobile deposits that have already cleared
Checks deposited at the bank
2️⃣ You received a cash or check payment and want to record it before depositing it
→ Use: Create a Payment for an Invoice
Common scenarios:
Cash payments received in person
Checks received by mail or in person
Money orders or cashier's checks
Any physical payment not yet deposited
3️⃣ You're depositing multiple checks or cash payments together in one bank deposit
→ Use: Record Multiple Payments in Bulk Deposit with an Undeposited Funds Account
Common scenarios:
Multiple client checks deposited together
Combination of cash and checks in one deposit
Weekly or daily batch deposits
Any situation where your bank shows one deposit but you have multiple invoice payments
4️⃣ Your client has a credit from a deposit or overpayment
→ Use: Apply an Existing Client Credit to an Invoice
Common scenarios:
Client prepayments or retainers
Overpayments from previous invoices
Refunds being applied to new work
Deposit credits being used for final invoices
How to Apply Payments
1️⃣ Link a bank transaction to an invoice (after deposit)
Use this method if the payment has already been deposited and appears in your bank feed.
Supported payment types:
Stripe payments: Credit cards, debit cards, ACH
PayPal payments: PayPal balance, credit cards, bank transfers
Traditional ACH: Direct bank-to-bank transfers
Wire transfers: Domestic and international
Digital wallets: Venmo, Zelle, Apple Pay, Google Pay
Mobile check deposits: Photos of checks deposited via banking apps
Traditional check deposits: Checks deposited at bank branches or ATMs
To link a downloaded transaction:
Go to Invoices in the left-hand panel
Find the invoice, click the three dots, and select Apply Payment → Link to Transaction
Choose the matching transaction, click Next, confirm the details, and click Save
🔄 This keeps your bank balance and invoice records in sync.
2️⃣ Create a payment for an invoice (before deposit)
Use this method if you've received a physical payment and want to record it before it's deposited.
Best for these payment types:
Cash payments: Any currency received in person
Personal checks: From individuals or businesses
Business checks: Company checks received by mail
Money orders: USPS, Western Union, or bank money orders
Cashier's checks: Bank-guaranteed payment instruments
Traveler's checks: Though rare, still occasionally used
To create and apply a payment:
Go to Invoices
Find the invoice, click the three dots → Apply Payment → Create Transaction
Enter the payment date, deposit account, and amount, then click Save
📝 Tip: Best for individual payments. For multiple payments in one deposit, use the bulk deposit method below.
3️⃣ Record multiple invoice payments in one bank deposit
(Using an Undeposited Funds Account)
Use this method when you deposit several client payments at once. Your bank will show one combined deposit, while your records should reflect individual payments.
💡 Example:
You receive three $500 payments and deposit them together
Your bank shows one $1,500 deposit
Your records show three $500 invoice payments
Without proper handling, reconciling this difference can be confusing. Using an Undeposited Funds account keeps everything aligned.
🛠 Set up an Undeposited Funds account
The Undeposited Funds account is not included by default — you'll need to create it the first time you want to use it. But don't worry — it's a quick, one-time setup. Once it's created, it will be saved in your account list and ready to use any time you record a bulk deposit.
Go to Add Account → Add Manual Account
Choose Other Business
Select Undeposited Funds
🔹 Note: This is not a real bank account. It's a temporary holding spot for payments received but not yet deposited.
✅ To record a bulk deposit using the Undeposited Funds account:
Go to Invoices
For each invoice, click the three dots → Apply Payment → Create Transaction
In the payment details, select Undeposited Funds as the Deposit To account
Deposit the checks together at your bank
When the combined deposit appears in your bank feed, categorize it as a Transfer to Undeposited Funds
📊 What This Does:
✅ Your bank account shows one $1,500 deposit
✅ Your invoice records show three $500 payments
✅ Everything reconciles — cleanly and accurately
❗ Forgot to use your Undeposited Funds account?
No problem — you can still split the bulk deposit after it hits your bank:
Open the downloaded bank transaction
Click the three dots → View Transaction → Split under Category
For each portion:
Select the correct Business Income category
Enter the amount
Check Invoice Payment
Link to the appropriate invoice
Click Save
4️⃣ Apply a client credit to an invoice
Use this method when your client has a credit on their account — from a deposit, prepayment, or overpayment.
Common credit scenarios:
Project retainers: Upfront payments for ongoing work
Overpayments: Client paid more than the invoice amount
Refund credits: Money owed back to client, applied to new work
Deposit credits: Partial payments made when work was commissioned
To apply a client credit:
Go to Invoices
Find the invoice, click the three dots → Apply Payment → Use Existing Credit (available credit(s) will be shown)
Enter the amount to apply to invoice and click Save
💡 Client credits are managed in the Clients & Projects section and can be applied in full or in part to any open invoice.
Advanced Payment Scenarios
Partial Payments
If a client pays only part of an invoice, record the partial payment using any of the above methods. The invoice will remain open for the remaining balance, and you can apply additional payments as they come in.
Multiple Payment Methods for One Invoice
Some clients pay invoices using multiple methods (e.g., partial check payment and partial credit card). Record each payment separately using the appropriate method above.
International Payments
For international wire transfers or foreign currency payments, use the "Link a Bank Transaction" method once the payment appears in your bank feed. Your bank will handle currency conversion.
Recurring Payments
For clients who pay the same amount regularly (retainers, subscriptions), you can set up recurring invoices and link payments as they appear in your bank feed.
💡 Best Practices
Record payments promptly: Don't wait until month-end to record payments
Match payment dates: Use the actual date you received the payment, not when you recorded it
Keep payment records: Store copies of checks, payment confirmations, and receipts
Reconcile regularly: Compare your invoice records to your bank statements monthly
Use consistent methods: Develop a routine for how you handle different payment types
🆘 Troubleshooting Common Issues
Problem: Payment appears in bank but doesn't match any invoice
Solution: Check if it's a partial payment, overpayment, or payment for multiple invoices
Problem: Client says they paid but no payment appears
Solution: Verify payment method and check if payment is still processing
Problem: Bank deposit doesn't match invoice total
Solution: Check for bank fees, returned check fees, or processing charges
Problem: Cannot find the payment transaction to link
Solution: Verify the payment has cleared your bank and appears in your downloaded transactions
By following this guide, you'll maintain accurate financial records and have a clear picture of your cash flow at all times. Remember: good payment tracking today saves hours of confusion later!