Customer unable to pay balance after partial payment made online

Good to see you here in the QuickBooks Community, @HHAvocado.

Let me help guide you about recording a partial payment from customer in QuickBooks Desktop. 

In cases like this, you can delete the customer's payment from online and manually received the payment in QuickBooks to record the amount as partial payment for an invoice.

To record a partial payment, here's how:

1. At the top menu bar, click Customers.
2. Go to Receive Payments.
3. On Received From drop-down, choose the customer’s name, then enter the partial Amount. 
4. Make sure the date is correct, then choose the Payment method.
5. Select the Invoice(s) to be paid by putting a check mark next to the invoice.
6. Select Save & Close.

For additional reference, you can check this article: Record a payment for an invoice. 

That should do it! Don't hesitate to leave a comment below if you have additional questions about the invoice payment. I'll be happy to answer them for you. Wishing you and your business continued success. 

Did as you said but e-invoice still says zero??

Thanks for joining this thread, Kitty111.

I appreciate you following the resolution steps provided by my colleague. Adding a manual payment directly to the Payments account can help resolve the issue.

The option to record a partial payment to the emailed invoices is unavailable at this time. Once a customer receives payment whether it’s partial or full, the transaction’s posting status will automatically be closed.

To track the remaining amount, manually add it in your QuickBooks Payments account.  Here's how:

1. Log in to your QuickBooks company file.
2. Choose the Banking tab located at the top menu bar.
3. Scroll to the middle and select Make Merchant Service Deposits.
4. Choose the Add Online Payments option, then input the deposit.

After entering it, this gives you an option to create an invoice. You’ll have to select the Need Invoice? link to make one.

Just in case, I also added a link with detailed information about recording Merchant Service deposits.

To record the amount, process it in your company file. Check out the steps provided by @JanyRoseB for visual reference or refer to this article for detailed instructions: Record a payment for an invoice. 

This information should get you on the right track. If you have further questions about the process, let me know by posting a comment below. I’m always here to help.

Adding a manual payment directly to the Payments account DOES NOT help resolve the issue.

I always enter all payments manually. I receive an email from Intuit that an invoice was paid from an email and I enter that payment manually. And every time I have a partial payment - it doesn't let the customer to pay the remaining balance. It will show in the subject line that there is a balance, but when they go to "View and Pay" it says "Paid in Full". Now they can't pay the balance, which is very inconvenient for both parties (us and customers).

Thanks for joining this conversation, SvetaZ.

As mentioned by my colleague above, recording a partial payment in QuickBooks Payments will automatically mark the invoice as closed or fully paid. That said, I'll send feedback regarding this to our Product Developers. They're always looking for ideas from users on how to improve QuickBooks.

In the meantime, I recommend visiting our Blog site. This is where we share recent happenings and future developments, such as updates to newly added features.

Just in case, I'll be adding these articles for future reference:

• Record an invoice payment.
• Let your customers pay invoices online.
• Common questions about paying invoices online.

Please know that I'm only a post away if you have any other issues or concerns. I'll be more than happy to assist. Have a good one!

I am having the same issue. 

Hi there, pitchess.

Thanks for joining the Community.

I'm backing up my colleagues' information that paying a partial payment in QuickBooks Payments will automatically mark the invoice as closed or fully paid. As an alternative, you'll need to manually track the remaining balance and add it to your QuickBooks Payments account.

You can refer to the steps provided above of my colleague @Rasa-LilaM.

Once done, you'll need to select an option Need Invoice? to create an invoice. Then your customer can pay now the remaining balance.

To know more about creating invoice payment in QuickBooks, check out this article for future reference: Let your customers pay invoices online.

If you need anything else, please post a comment in Community. We are here to back you up. Have a good one!

I realize I had the same problem. I have notice that the payment was recorded twice, so I check on merchant service center to see if I receive the payment twice. And I didn't, so I delete the payment that I was not accounted for on the MSC. 

Hope this helps.

I am experiencing the same issue and thinking not to use Intuit to collect payment. This is very ridiculous that partial payment will automatically mark the invoice as closed or full paid. It causes confusion to customers, inconvenience to business owner as well as providing an excuse/chance for business owner to use other third party, like Paypal to collect customers payments. I just do not understand why it is so difficult for your Tech team to find a solution.   

I am experiencing the same issue and thinking not to use Intuit to collect customers payments anymore. It is very ridiculous that partial payment will automatically mark the invoice as closed or fully paid. It causes confusion to customers, inconvenience to business owners as well as providing a chance for business owner to switch Intuit to other third party agency, such as Paypal. Intuit is a big company and this should be a very minor issue to your Tech team. Just do not understand why it is still an issue nowadays.    

This issue is ongoing. I use Quickbooks Desktop Enterprise and regularly send invoices via email with the option to pay via ACH. If the customer makes a partial payment as opposed to a full payment the link and that invoice is essentially broken permanently regardless of how the payment is recorded. I've added the payment from the merchant center, and recorded it manually. The workaround I use for customers that want to make multiple ACH/CC payments is to duplicate the invoice, move the previous payments to the new invoice, and then create a balancing credit against the original invoice. This is time consuming, a recording nightmare of a mess, and extremely frustrating for me on top of being confusing and unprofessional for customers to deal with. This is not a user error, it is a technical error I desperately wish Intuit would resolve. 

This has become a BIG problem. Here's our issue: Invoice total $1200 Customer pays $500 partial payment/deposit with credit card online so balance is $700. When we send the invoice for final payment QB is applying the initial $500 payment to the $700 balance (not the $1200 invoice total)so customer can only pay $200 of the remaining $700 balance. We've tried everything including manually entering payment and nothing works. PLEASE advise if there is a solution. This has become a significant issue for us and affecting our ability to collect payments in full.

Good Afternoon, @JB94. 

Thanks for joining in on this thread. This sounds like an error within our system. Don't worry. We can try a few basic troubleshooting steps to help fix this problem. 

First, let's create a back up of your company file. Here's how: 

1. Go to the File menu. 
2. Pick Switch to Single-user mode. 
3. Go through step 1 again. 
4. Hover over Back up Company and then tap Create Local Backup. 
5. Click Local Backup and then Next. 
6. Choose Browse and where you want to save your backup company file in the Local Backup Only section. 
7. This runs a test to make sure your backup file is in good shape before you save.
8. Press OK. 
9. Hit Save it now and Next. 

Afterward, delete the partial payment and invoice, and then recreate them. You can also choose credit card without processing it again. Here's a link that may come in handy: Record an invoice payment. 

Let me know if you need help with anything else QuickBooks. I'm always here to lend a helping hand. Have a fantastic weekend!

Thank you Candice for your reply. Unfortunately we have tried deleting the invoice and payment and starting over. Still cannot pay the accurate balance online. To be clear, this is not a new problem nor is it an isolated issue. It happens on every invoice where a client pays a partial payment online. Same as described in the posts above by "Kasty" and "Hua101" which leads me to believe it is an intuit problem perhaps without a solution. Please research and advise if this is the case so I can look for a work around. 

Thank you for connecting with us once again, JB94. If you are using Merchant Service, you will be allowed to receive partial payments. However, our QuickBooks system doesn't allow this to happen currently. Instead, it marks the invoice as paid in full. Therefore, the customer would need to pay in full.  

A workaround could be to divide the invoice into multiples to account for each partial payment (basically having separate invoices). I recommend browsing through this article that explains how to record an invoice payment for your edification.

If you have any questions or need clarification on partial payments, please let me know below. We are here to help! Take care, and enjoy your weekend. 

I'm sorry but that answer is ludicrous.

We are all trying to streamline our workload not add to it, not forgetting of course that we would pay additional fees if we split the invoice into multiples!

This is just not helpful...

Thank you for your response.  Definitely not the answer I was hoping for but I had a feeling. I have to assume this will be at the top of the suggestion list for the next upgrade as it is an integral part of conducting business especially a service business where it is customary to pay a deposit on an invoice and then pay the balance when job is complete. 

Listen you F*(^%$# Morons at Quickbook's, dont f@cking charge us $3.00 ACH payments fees if you cant get your f&cking sh!t together and allow customers to make partial like every other f@cking payments network around. What kinda sh!t show is intuit running over there, its NOT 1992 f$ckheads. fix the f@cking link so if you send a customer a $1000 invoice and they pay $500 ACH, when they are ready to pay balance they can click link again and pay balance. Dumbf&cks! 

We just began using the online payment portal a few weeks ago and I just encountered this issue, and I must say it is a very unprofessional glitch that effects business' cash flow and misleads our clients. I can't believe this was first reported back in 2019 and has still not been resolved. Our customer made a partial payment on their invoice, which the embedded online payment link initially offers them the option of making a partial payment. Then when they return to make the another payment it says 'PAID Balance Due $0.00' with the Invoice number, and amount listed (which is the full initial invoice amount, not the amount they paid). Apparently it is an automatically generated page telling them nothing else is due, even though a balance is due. If the customer was not honest, they easily could claim they paid the full invoice according to the information on the page generated by Intuit. 

Total failure for QB.  But I found a round about solution until they fix it. 

1.  Go to the original invoice.

2.  click "Create a Copy" (but make a note of the invoice # of the original!) this will bring you from the original to the new invoice and will have a new invoice #.

3.  Click "Save & New".

4.  Bring up the original invoice and delete it.  It will tell you that it will leave a credit of the original partial payment on the customer's account.

5.  Bring up the new invoice that you had created. 

6.  Change the invoice number to the number from the original invoice.

7.  Click on "Apply Credits". (the remainder of this step is self-explanatory)

8.  Email the new invoice to your customer.  They are now able to pay the remaining balance online.

I know this is a pain but at least it is a solution... and hopefully VERY temporary!

This is annoying. We don't want 2 invoices for one job and we don't want to delete payments or invoices. We don't want to tell customers to switch browsers or go incognito, which doesn't work anyway. Just make it seamless for us to receive payments.

We especially don't want customers erroneously told their invoice is paid when it is clearly not. It not only won't let the customer pay, it tells them the invoice is paid. Please fix this.

I do this too but it's such messy bookkeeping.

Yes, same unprofessional problem. We are looking at other accounting software. Hope to find something that's in the 21st century. 

Hello.  Did you find another payment collection ACH/CC service that works?  Thanks