QB Payment Link Not Applying to Invoice?

Hello, @EthanDale.

I'll be glad to help you apply payments to an invoice in QuickBooks Online.

Excessive historical data kept in your browser might cause problems like these. I recommend performing some basic troubleshooting procedures to see whether your problem is browser-related.

Start by logging into your QBO company using an incognito browser. Here's how:
 

• Chrome: Ctrl+Shift+N
• Firefox: Ctrl+Shift+P
• Safari: Command+Shift+N
   

If this works, I recommend clearing the regular browser cache. This will avoid the browser to behave strangely. Otherwise, kindly use another supported browser. Once done, you can follow the steps in this article to manually record the payment to mark the invoice as paid.

Here's how:

1. Tap + New.
2. Choose Receive payment.
3. From the Customer dropdown, tick the name of the customer.
4. From the Payment method dropdown, hit the payment method.
5. From the Deposit to dropdown, select the account you put the payment into.  
6. In the Outstanding Transactions section, tap the checkbox for the invoice you're recording the payment for.
7. Enter the Reference no. and Memo if needed.
8. Click Save and close.

I also encourage you to visit this resource that will guide you in personalizing sales forms: Customize invoices, estimates, and sales receipts in QuickBooks Online.

Furthermore, I added this article for your reference to learn when QuickBooks deposits customer payments into your bank account: Find out when QuickBooks Payments deposits customer payments.

Feel free to add a reply if you have more questions about payments. The Community always got your back. Stay safe!

Hello,

This is not an issue with browser cookies or history. What I'm saying is that if a customer pays through a payment link, it does not show up as a "second payment" on the invoice. It shows up as a totally separate payment, and the invoice itself still shows them as having a balance.

I can help you apply the payment to the invoice, EthanDale.

If you created an invoice, you don't need to send a Payment link. Instead, add an Online payment option to an invoice.

Please note that when sending a payment link to your customer, QuickBooks automatically generates a sales receipt.

What you can do is delete the sales receipt and manually apply for the payment as partial payment via Receive payment. Let me walk you through how: 

To delete a sales receipt:

1. Go to the Sales menu then All sales.
2. Locate and open the Sales receipt.
3. On the Sales Receipt window, click More at the bottom.
4. Select Delete. Click on Yes to confirm.

To record partial payment for an invoice:

1. Click + New and select Receive payment.
2. From the Customer drop-down, select the name of the customer.
3. From the Payment method drop-down, select the payment method.
4. Select the account you put the payment into from the Deposit drop-down.
5. Enter the amount your customer paid.
6. In the Outstanding Transactions section, select the checkbox for the invoice you're recording the payment for.
7. Select Save and close.

For more details, check this article: Receive invoice payment in QuickBooks Online.

I am also adding this article about how QuickBooks Payments deposits work in QBO: Common questions about payments deposits in QuickBooks Online.

Get back to this thread if you have additional questions about the process. I'll be around to back you up.

I too ( and many other users, I'll bet) have same issues with dysfunctional/unusable QBO "features". 

Cleverly disguised and misrepresented as helpful tool, QBP payment links and online invoice payments do NOT attach/post or in any way record to actual invoices.  Seems like ALL payments apply as lump sum balance. Seriously? Unbelievable! What accounting or intelligent bookkeeper would design system this way?

So if online payment links are sent to client and they pay, even if invoices are shown in payment portal prior to payment, the funds do not auto attach to specific invoices.   Worse, send payment request with a flat amount QB automatically creates a sales receipt for that amount when YOU ALREADY HAVE INVOICES WAITING.  Workaround..  delete sales receipt then apply payments manually through deposit, otherwise you end up with double expensed items.   WT?!?!?   

If you try enabling auto apply credits in settings (thinking vendor credits) be prepared for incoherent, overpriced QB to then randomly apply client payments anywhere for that client, resulting in tons of partial payments all over the place. 

Neither options provide clarity for clients or frustrated QBO users.

That QB defaults to these barely>non-functional settings and lack of options is ridiculous.  Emailed emailed notifications from QBP/QBO web version do NOT offer any invoice/payment detail via reports, QBP useless portal or within QB or anywhere.  However, alerts from QB mobile app notifies of exact payment, client/payee AND WHICH ITEM WAS PAID.    Basic functionality does not exist for QBO 

Have you found any solution to this yet? 

We've come to help, @JkWilson. Let me chime in and provide additional information on how we can link the last payment to an invoice in QuickBooks Online (QBO) using QuickBooks Payments.

As of now, we're unable to link the final payment to close out the invoice. However, it will become a separate payment, which we can use as a credit to mark the invoice as paid. 

To do that:

1. Select + New and click Receive payment.
2. Enter the customer's name and the payment date.
3. In the Outstanding Transactions section, choose the open invoice.
4. In the Credits section, select the final payment we received using QuickBooks Payments.
5. Fill out the rest of the form, and leave the Payment method, Reference no., Deposit to, and Amount received fields blank.
6. Ensure the total is correct after applying for the credits.
7. Once done, please select Save and close.

Furthermore, the Undeposited Funds account records payments in QBO until we deposit them physically at your local bank. Banks frequently combine all of your deposits into a single transaction. We can do the same in QBO once we have your deposit slip and know which payments your bank combined.

You can always get back to us if you have additional questions about receiving payments. I'd be more than glad to assist you. Stay safe, and have a great day.

When the invoice is generated it is recorded as sales and when the payment is received it is recorded as income with the result the income is double the actual amount! Am I missing a step?

My pleasure to have you in this thread today, @sw1. I can help you fix the double income posted to your account for your invoice and payment entries.

Once you use QuickBooks Payments, your customers can pay their invoices online. The invoices will be marked as paid automatically unless you'll opt to process the payment for them.

To avoid generating double income for your invoices and payments, match the transactions under For Review don't add them. Here's how:

1. Sign in to your QuickBooks Online (QBO) account.
2. Click on Banking at the left pane, then go to the Banking page.
3. Select your account.
4. Look for the transaction posted to your bank.
5. Tap on the Find Match button.
6. Review the Matching records found in QuickBooks. This is the possible matching transaction you already entered in QuickBooks. You can also click on Find other matches to look for other entries.
7. Select the transaction, then Save.

However, if the transaction was already added to QuickBooks through the Add feature, you can undo the process by following these steps:

1. Go to the Categorized section.
2. Locate the transaction.
3. Click Undo under Action.

After that, replicate the steps provided above to match your entries. You may also review the resources from this link for more information: Categorize and match online bank transactions in QuickBooks Online.

On the other hand, if there are possible discrepancies in the amounts that include fees, you can always resolve the difference from the Match transactions window.

When you're ready to reconcile your account to match your bank statements, run through the topics from this link as your guide: Reconcile an account in QuickBooks Online.

If you have other QuickBooks questions in mind, let me know by leaving a comment below. I'm always here to help. Have a good one!

Perhaps I am misunderstanding? Please clarify how your process alleviates the duplicated revenue booked when QB Payment Request Sales Receipts posts and is matched to QBP from bank feed?  This matches payment amounts received to bank (good for bank rec maybe, but records revenue (in my case) to services.

Meanwhile all invoices (many with multi-lines and categories) remain unpaid.

So now sales receipt of payment co-exists with open invoices, unless Sales Payment Receipt is voided/deleted or all invoices are.  WHY ?

Invoices contain detailed data which needs to be retained, and often are integrated with a more sophisticated 3rd party integration. QBO deleting sales receipts could alter/remove stored client payment info (cc/ach etc).

Recently saw post that QB payment receipts are now unable to be deleted?

So QBO is forcing paying subscribers to delete key billing invoices to force users to only/always use crappy, dysfunctional QB payments  sales receipts vs competitors.

This issue has been ongoing for years all over the internet, and still a major frustration with many users forced to beg other users on a community to disguise how incoherent, near useless and greedy intuit is.

The dysfunctional "features" and utter arrogance and disregard Intuit continues to show for paying subscribers really warrants a class action lawsuit for deliberately blocking 3rd party payment processors and all of the wasted time for us to continually have to seek assistance as QB rolls out more unusable features to drum up fees without culpability and a workable accounting system.

So HOW to resolve this without deleting invoices/documents? 

Many posts about this, but nothing works.

Have used many accounting packages and NEVER been advised to delete invoices in order to apply an electronic or other payment.

Especially with the only purpose being to force QBP and increase intuit's bottom line while they hog all credit card fees by manipulation and convolution.

The fact that we are all forced to use so many 3rd party add-ons to achieve basic functionality says it all.

I hear your thoughts regarding QuickBooks Payments, Jolie. Let me share some workarounds to fix duplicate revenue and keep your transactions in place.

I understand that you don't desire to delete any of your transactions for recording purposes. I want you to know that the only way to fix duplicate income is to match them from the Banking page or remove the other record from your account. Great news! Aside from deleting your invoices or sales receipts, you can void them instead. This way, you'll still have a record of the transactions without causing double amounts since voided entries won't affect your account balances or reports.

To start:

1. Open your transaction.
2. Select More in the footer area.
3. Tap on Void or Delete.
4. Hit Yes to confirm the action.

To know more about the process, you can open this article: Void or delete transactions in QuickBooks Online.

On the other hand, these materials will give you additional hints while processing online payments for your customers' invoices: 

• Take and process payments in QuickBooks Online with QuickBooks Payments
• Common questions about payments deposits in QuickBooks Online

It isn't the impression I want you to have. I want you to know that our doors are open 24/7 to help if you have follow-up questions while using QuickBooks as part of your business. Keep safe!

What is the process AFTER a transaction has been RECONCILED to  Undo the transaction that was automatically recorded as Undeposited funds because of an online QuickBooks payment to an invoice.  The invoice was closed out by the payment but the register shows as Undeposited Funds?  What is the process when that month has already been reconciled? How do i get the the amount out of Undeposited funds after reconciliation?   This occurs because QBO puts a Sales Receipt for an online QB payment instead of covering the invoice.  Why would it call it undeposited funds when QB automatically deposited it?  I don't catch this undeposited funds entry until after I have reconciled because the entries were done automatically.  If I do catch the payment going into undeposited funds, i have to go through several steps to fix it.  How can we stop QBO from automatically creating sales receipts and putting the payment in undeposited funds? I would rather manually match everything myself.   

I understand the challenges and confusion that can arise when dealing with reconciled transactions ending in Undeposited Funds in QuickBooks Online (QBO), Alan. I'm here to share insights about this. 

We can undo reconciled transactions even after the month has been reconciled. We can go to the  Chart of accounts, find the account with the reconciled transaction, and view the register to locate the transaction marked as reconciled. Then, remove the checkmark in the column with the "R" until it's blank, and save the changes.

After unreconciling the transaction, review your accounts to ensure they are balanced and accurate. If there are still issues or if you need to undo multiple transactions, I suggest reaching out to your accountant for further assistance.

To get the amount out of undeposited funds, we can create a bank deposit. Ensure that the total amount in the deposit matches what you are moving out of Undeposited Funds.

Here's how:

1. Go to +New and select Bank Deposit. 
2. Choose the account where you want to deposit the funds.
3. Select the payments from Undeposited Funds that you want to include in this deposit.
4. Enter the necessary details like the date, payment method, and amount.
5. Click Save. 

Undeposited funds is a term used in QuickBooks Online to track payments until they are deposited into your bank account.

When you process a payment with QuickBooks Payments, QuickBooks automatically creates a sales receipt and deposits the payment into the Undeposited Funds account. This is to ensure that the payments are properly recorded and matched with the corresponding invoices when you make a bank deposit

To prevent them from automatically creating sales receipts and putting payments in Undeposited Funds, you'll need to manually match the transactions.

I've added some helpful resources to learn more about correcting issues when reconciling QuickBooks accounts, and viewing details for missing reconciled transactions or reports in QuickBooks Online.

• Fix issues at the end of a reconciliation in QuickBooks Online
• How to view details for missing reconciliation reports or reconciled transactions

If you have any other concerns with reconciling transactions in QBO, please let me know, and I'll do everything I can to help here in the Community.