Critical Financial Report Issues After Updating to WHMCS 9.0.0

[websavers]

16 hours ago, Hmmcrunchy said:

is this a version 9 special as well? suddenly we are getting clint not able to simply pay by paypal - and its coming up with link your account instead of just sending over to paypal for authorisation 

This was changed in 8.9 with PayPal Payments addition: https://docs.whmcs.com/releases/8-9/8-9-release-highlights/

It makes it so that if you change the price of a service after first payment, you can capture the new amount upon renewal, without it only capturing the old amount then having to get payment for the rest from the customer. This one is actually a welcome improvement (IMO).

[CycloneServers]

I would also like to note that when a client cancels a service and later requests that the cancellation be revoked so they can continue using the service, the system prevents them from making payment due to the credit note being applied. The invoice becomes closed and locked, which prevents the client from paying for the service.

Unfortunately, this behavior appears to be a result of the recent update. In our experience, the change has created several operational issues and does not appear to have been fully tested prior to release.

[Paulo Nichio]

Thank you for the terrible WHMCS support. This is now the tenth client who has made a bulk payment and the late fee is simply not added to the invoice, and none of the outstanding invoices are automatically marked as paid.

I’m not even going to mention the credit and debit issues anymore, because it seems the WHMCS developers themselves don’t even know what they’re doing.

Does anyone have a suggestion for another system similar to this garbage?

[WHMCS John]

On 2/24/2026 at 8:32 AM, Hmmcrunchy said:

ok even more worrying 

we have just had a clients invoice randomly paid by a credit note!! we didn't apply the credit note, we don't know where this random credit note came from, its not shown in the "Manage Credits" 

If fact on further investigation it seem us marking an invoice as paid (if its a bank transfer)  it is creating new credit notes and applying them to the invoices as its paid and not marking it as bank transfer ?! 

Worst still this is going out to the client via email as Ledger adjustment on the invoice receipt - not a payment, so they are getting in a muddle as well !

this does need to be fixed pretty damn fast please @WHMCS John!

We are just taking over a company and repair shop at the moment so this is literally the worst possible time for us to seem like we are a bunch of unprofessional idiots due to nonsensical invoices going out. 

im just about to transfer in 150 clients but we may have to hold this up or look to move to another system as we just cant have this ...

I can confirm the recommended method to record bank transfer payments has always been via the "Add Payments" tab on the invoice page. The Transaction ID isn't a required field if you don't have a reference for the payment.

We will update the popup message to make it clearer that in v9, the "Mark Paid" button issues a credit note for the invoice balance (case WHMCS-25149).

 

On 2/27/2026 at 8:41 AM, Hmmcrunchy said:

is this a version 9 special as well? suddenly we are getting clint not able to simply pay by paypal - and its coming up with link your account instead of just sending over to paypal for authorisation 

I can confirm this is the design of the latest "PayPal Payments" module. It enables you to charge client's Payal accounts on demand and is the recommended payment flow from PayPal these days.

  

On 3/4/2026 at 2:44 AM, CycloneServers said:

I would also like to note that when a client cancels a service and later requests that the cancellation be revoked so they can continue using the service, the system prevents them from making payment due to the credit note being applied. The invoice becomes closed and locked, which prevents the client from paying for the service.

Unfortunately, this behavior appears to be a result of the recent update. In our experience, the change has created several operational issues and does not appear to have been fully tested prior to release.

The process in this situation is the same in v9 as v8 and earlier:

1. Edit the service record and move the Next Due Date forward/back by 1 day,
2. Ensure the status is Active or Suspended
3. Save Changes
4. Click "Generate Due Invoices"

The system will generate a new invoice for the previously cancelled item for the client to pay.

 

On 3/4/2026 at 5:22 AM, Paulo Nichio said:

Thank you for the terrible WHMCS support. This is now the tenth client who has made a bulk payment and the late fee is simply not added to the invoice, and none of the outstanding invoices are automatically marked as paid.

I’m not even going to mention the credit and debit issues anymore, because it seems the WHMCS developers themselves don’t even know what they’re doing.

Does anyone have a suggestion for another system similar to this garbage?

We have released v9.0.2 which addresses the matter of late fees in mass pay invoices (case WHMCS-25149).

 

[nmdpa3]

If you’re going to market a platform as a professional billing system, then act like one.

That means involving certified accountants, validating against real-world accounting standards, and subjecting every financial change to rigorous testing before it ever reaches production. Anything less isn’t just an oversight — it’s negligence.

Rolling out changes with this level of impact, only to expose fundamental bugs, is completely unacceptable. Billing systems are not feature playgrounds. They are the financial backbone of businesses that rely on accuracy, stability, and trust.

What’s most concerning is not just the presence of these issues — it’s that they made it through your release process at all. That speaks to a breakdown in quality control, testing discipline, and respect for your user base.

We’ve deliberately held off upgrading to 9.x while waiting for critical modules to catch up. Based on what we’re seeing now, that decision looks more justified than ever — and we’ll be waiting considerably longer.

If you want to be taken seriously in this space, raise the bar. Because right now, this isn’t it.

[sol2010]

I have yet to upgrade - but from what I am reading it sounds like another horror show mess.

WTF is with the massive change to the immutable financial system? Why has this not been flagged and professional advice sought - sounds like another dogs dinner.

"no edits" to the invoices - is that really true? We use the edit invoice feature frequently and this is not a feature I am willing to lose. 

$allow_adminarea_invoice_mutation = true;  Does this solve the issue? 

 

[Hmmcrunchy]

On 3/19/2026 at 5:23 PM, WHMCS John said:

I can confirm the recommended method to record bank transfer payments has always been via the "Add Payments" tab on the invoice page. The Transaction ID isn't a required field if you don't have a reference for the payment.

We will update the popup message to make it clearer that in v9, the "Mark Paid" button issues a credit note for the invoice balance (case WHMCS-25149).

 

I can confirm this is the design of the latest "PayPal Payments" module. It enables you to charge client's Payal accounts on demand and is the recommended payment flow from PayPal these days.

  

The process in this situation is the same in v9 as v8 and earlier:

1. Edit the service record and move the Next Due Date forward/back by 1 day,
2. Ensure the status is Active or Suspended
3. Save Changes
4. Click "Generate Due Invoices"

The system will generate a new invoice for the previously cancelled item for the client to pay.

 

We have released v9.0.2 which addresses the matter of late fees in mass pay invoices (case WHMCS-25149).

 

Thank you for the reply @WHMCS John and for getting back to me about the credit note issue. 

Just a bit of feedback, for me personally ( our accounts dept are happy to do the add payment)  if would be a lot easier if you  could tick a set of invoices and mark them paid -  it would then show them paid with the method stated on them (eg bank, cheque etc) rather than having to go into say 80 invoices individually to add a payment to each one 

[joeroot6543]

On 2/6/2026 at 7:00 PM, Paulo Nichio said:

I have updated my WHMCS installation to version 9.0.1 and noticed that some of the previously reported issues have indeed been corrected. The debit and credit values are no longer being incorrectly counted in the financial reports, the homepage billing widget, or the “Transactions” tab within the client profile, which is a positive improvement.

However, the issue related to invoice cancellation still persists. When a client requests a cancellation, for example, we are still unable to properly cancel the issued invoice.

As a workaround, I added the following line to the 'configuration.php' file:

$allow_adminarea_invoice_mutation = true;

After adding this setting, the invoice can be cancelled. However, the system continues to generate multiple credit notes, even though these are no longer reflected in the reports. This behavior is particularly concerning because these credit entries remain visible on the client’s invoice, and the client may reasonably question why a cancelled invoice shows applied credit entries.

In practice, the behavior is as follows: the client requests a cancellation, the invoice cannot be cancelled normally, and each attempt to cancel the invoice results in a new credit note being created. If the cancellation is attempted multiple times, multiple credit notes are generated. When the configuration option is enabled, the invoice can finally be cancelled, but a credit note is still added regardless.

This creates confusion both internally and for the client, as it gives the impression that credits were issued when, in fact, the invoice was simply cancelled and no credit should have been generated at all.

Although the recent update addressed part of the problem, this remaining behavior continues to affect invoice integrity and client transparency.

I’m actually experiencing something very similar after upgrading, and I have the same question because the financial inconsistencies are really concerning. The way certain transactions are being classified just doesn’t make sense from an accounting perspective, especially things like late fees showing as “Amount Out” or cancelled invoices appearing as income. It makes it really hard to trust the reports or use them for any kind of real decision-making.

What’s also frustrating is the lack of a clear update or workaround, especially if support has already confirmed it’s a critical issue. I’m in the same position where I’m double-checking everything manually just to be sure the numbers are accurate, which defeats the purpose of having an automated system. Really hoping others can share if they’re seeing the same behavior and whether there’s any temporary fix or timeline for a proper resolution.

[SeanP]

Are there still issues after the 9.0.3 release?

[CycloneServers]

58 minutes ago, SeanP said:

Are there still issues after the 9.0.3 release?

Nothing has changed still the same issues.  

[sol2010]

@WHMCS John It's disappointing to see issues and bugs being introduced with no update or resolution planned. The invoice and billing aspect of WHMCS worked fine as it was.

In particular, it's a huge timesaver being able to quickly manually mark multiple invoices as paid on the invoices (or outstanding invoices) page.

Can you confirm if this behaviour could be reinstated - or is there another way to mass update invoices without creating credit notes?

[sol2010]

On 4/1/2026 at 8:23 PM, Hmmcrunchy said:

Thank you for the reply @WHMCS John and for getting back to me about the credit note issue. 

Just a bit of feedback, for me personally ( our accounts dept are happy to do the add payment)  if would be a lot easier if you  could tick a set of invoices and mark them paid -  it would then show them paid with the method stated on them (eg bank, cheque etc) rather than having to go into say 80 invoices individually to add a payment to each one 

This is essential for us and was easy pre 9

[joeroot6543]

On 4/13/2026 at 11:54 PM, joeroot6543 said:

I have updated my WHMCS installation to version 9.0.1 and noticed that some of the previously reported issues have indeed been corrected. The debit and credit values are no longer being incorrectly counted in the financial reports, the homepage billing widget, or the “Transactions” tab within the client profile, which is a positive improvement.

However, the issue related to invoice cancellation still persists. When a client requests a cancellation, for example, we are still unable to properly cancel the issued invoice.

As a workaround, I added the following line to the 'configuration.php' file:

$allow_adminarea_invoice_mutation = true;

After adding this setting, the invoice can be cancelled. However, the system continues to generate multiple credit notes, even though these are no longer reflected in the reports. This behavior is particularly concerning because these credit entries remain visible on the client’s invoice, and the client may reasonably question why a cancelled invoice shows applied credit entries.

In practice, the behavior is as follows: the client requests a cancellation, the invoice cannot be cancelled normally, and each attempt to cancel the invoice results in a new credit note being created. If the cancellation is attempted multiple times, multiple credit notes are generated. It almost feels like working with a morse code tapping translator each tap (or cancellation attempt) is being registered multiple times, producing repeated or unintended outputs instead of a single, clear result. When the configuration option is enabled, the invoice can finally be cancelled, but a credit note is still added regardless.

This creates confusion both internally and for the client, as it gives the impression that credits were issued when, in fact, the invoice was simply cancelled and no credit should have been generated at all.

Although the recent update addressed part of the problem, this remaining behavior continues to affect invoice integrity and client transparency.

STILL Facing this issue!

[ToddTB]

Glad I still haven't updated from 8.13.1    ....  my biggest issue is the lack of ability to edit an invoice. It sounds like there are still many reasons not to upgrade. If they wanted to improve accounting features than add common financial reports like MRR/ARR etc.... relying on Metricscube to supply common reports is silly. 

[Ahez]

Still not same. we are moving to clientex. whmcs is going to end not listing only taking money.  

[SeanP]

What issues still remain on the 9.0.4 release?

[Damo]

All issues remain on 9.0.4.  It was a security release, nothing more, see https://blog.whmcs.com/133788/whmcs-904-and-8133-maintenance-releases

[sol2010]

So Basically a massive FU from the whmcs staff who have neglected to address any concerns.

 

[SeanP]

It looks like they released several maintenance releases, with some addressing issues reported in this post (9.0.1, 9.0.2, 9.0.3).  I was just wondering if anyone had a current list of what was still broken after the last maintenance release.  Are we saying nothing has been fixed since the initial release of 9.0?  None of the maintenance releases actually fixed anything?

[bluesteam]

On 4/1/2026 at 9:23 AM, Hmmcrunchy said:

Thank you for the reply @WHMCS John and for getting back to me about the credit note issue. 

Just a bit of feedback, for me personally ( our accounts dept are happy to do the add payment)  if would be a lot easier if you  could tick a set of invoices and mark them paid -  it would then show them paid with the method stated on them (eg bank, cheque etc) rather than having to go into say 80 invoices individually to add a payment to each one 

So after we have been told to rather use the Add Payment method instead for every single individual invoice, up to now for 15 years I have ALWAYS used the "Mark Paid" option for bank transfers as this is genuinely helpful when you have 5 invoices that need to be marked as paid. Now I have to edit every single invoice and mark them paid manually. What a MESS!!

But now how do we fix the invoices that have credit notes added to them that are not being included in the reporting that were all marked with "Mark Paid" button?

We can't edit the invoice after it has already been marked as paid and emails and invoices receipts have already gone out to clients!

Did you manage to rectify the ones that have credit notes and were marked paid using the "Mark Paid" button so it shows in the financial reports?

Do we just mark them as UNPAID and then add a payment? or what?

Edited yesterday at 06:19 AM by bluesteam

[Damo]

WHMCS support have told me recently that they're focusing on support tickets, and this community is not a good way to obtain support. Send a support/bug report and include the URL to your post and they will reply. 
Would be great if you post the reply here too. Will most likely be a case/bug number for a future release. 

[sol2010]

16 hours ago, bluesteam said:

So after we have been told to rather use the Add Payment method instead for every single individual invoice, up to now for 15 years I have ALWAYS used the "Mark Paid" option for bank transfers as this is genuinely helpful when you have 5 invoices that need to be marked as paid. Now I have to edit every single invoice and mark them paid manually. What a MESS!!

But now how do we fix the invoices that have credit notes added to them that are not being included in the reporting that were all marked with "Mark Paid" button?

We can't edit the invoice after it has already been marked as paid and emails and invoices receipts have already gone out to clients!

Did you manage to rectify the ones that have credit notes and were marked paid using the "Mark Paid" button so it shows in the financial reports?

Do we just mark them as UNPAID and then add a payment? or what?

Are you able to actually just delete these invoices and credit notes - even through the database?

It's very frustrating to be forced into this massive change.   I guess the answer for the moment is to not upgrade from 8.13.4 (maybe you can downgrade back to 8.13.4 - if it is safe to do so -  It does have Long Term Support still)

@WHMCS John why can't you ... 

Version 9.1 - option to join or not to join, immutable invoicing.

Our invoicing system is handled by Xero so these immutable invoicing changes are just added complexity we don't need.

Edited 11 hours ago by sol2010

[bluesteam]

7 hours ago, sol2010 said:

Are you able to actually just delete these invoices and credit notes - even through the database?

It's very frustrating to be forced into this massive change.   I guess the answer for the moment is to not upgrade from 8.13.4 (maybe you can downgrade back to 8.13.4 - if it is safe to do so -  It does have Long Term Support still)

@WHMCS John why can't you ... 

Version 9.1 - option to join or not to join, immutable invoicing.

Our invoicing system is handled by Xero so these immutable invoicing changes are just added complexity we don't need.

The invoices and receipts have already gone out to the clients so deleting invoices is a no go I'm afraid. I suspect I am going to have to figure out a way to edit the invoice and remove the credit note and then add a payment.

I have opened a ticket but support doesn't seem to see the issue clearly. The support staff member is telling me the following:

 

Quote

Hi there,

Thank you for contacting WHMCS.

The figures in WHMCS appear consistent: your Admin Dashboard shows R####### for this month, and your Annual Income Report shows the same (R####### Amount In, less R##### fees = R####### Balance). Both are reading from the same source.

I believe the difference comes from the table your query was using. Your query was summing paid invoice totals from tblinvoices, which reflects invoices marked as Paid — in your case, R####### for that period.

However, income reports do not use tblinvoices. For income and accounting purposes, what matters is actual money received, and that is stored in tblaccounts. As WHMCS documents, the Annual Income Report is "a report of the received income for the year by month... It includes your recorded transactions."

In short: tblinvoices tells you which invoices are marked Paid; whereas tblaccounts tells you what was actually received. For income reporting, this is based on the latter, which is why your query and the reports show different numbers.

Nevertheles, for tax/accounting purposes, the more useful reports are:

• Reports > Income > Monthly Transactions (daily payment activity)
• Reports > Exports > Transactions (full transaction export for your date range)
• Reports > Income > Annual Income Report (monthly cash received)

These reflect actual money received rather than invoice issuance or paid status alone.

If you need reporting tailored to your own requirements, WHMCS reports can also be customised (on self-hosted installations) where you can modify the built-in reports or create new ones.
For further information, visit:
https://docs.whmcs.com/9-0/customization/custom-reports/

I hope this helps, and if I can be of further assistance, please let me know. Thanks.

Kind regards,

The person doesn't seem to understand my problem so I am still going back and forth with them at this stage.