First, do a normal pay run to pay the employee anything they're owed for the current pay period, up to their last day at work.

It's best to do this separately, before you do their final pay, so that they accrue all the leave they're owed for the time they've worked. It also means you'll be able to clearly show what makes up their final pay.

Don't include any of their unused leave in this pay run.

After you've paid the employee's final standard pay, you can work out how much paid leave they're owed so you can pay it out.

You can see these amounts in the Payroll details tab of their employee record, in the Leave tab. Make a note of the total hours of accrued leave that you'll need to pay out, like annual leave.

Do they have long service leave? Long service leave rules vary from state to state, so if you need help working out a payment for unused long service leave, speak to your accounting advisor.

You'll need to set up pay items for each type of unpaid leave you'll be paying out to the employee. This makes it clear on the employee's pay slip what they're being paid, and also ensures that superannuation and leave isn't accrued on the unused leave payments.

Go to the Payroll menu > Pay items and click the Wages and salary tab. Click the Unused Annual Leave pay item, or create it if it doesn't exist yet. Make sure:

• the Pay basis is set to Hourly
• the right ATO reporting category has been chosen.
• the Pay rate is set to Regular rate multiplied by, with a value of 1.0000

Next, under Employees using this pay item, assign this pay item to the employee you're paying out then click Save.

Do this again for any other types of leave that need to be paid out to the employee, like unused long service leave.

Super and leave shouldn't usually be calculated on unused leave payments. Your pay items might already be set up to prevent this from happening, but you should check to make sure.

You'll do this by adding exemptions for the unused leave pay items on the Superannuation and Leave tabs of the Pay items page.

For each superannuation pay item that applies to the employee (such as Superannuation Guarantee):

• Make sure the Exemptions section contains all the unpaid leave items you set up in step 3.
• If they're not all there, click Add exemption to add them.

For each leave accrual pay item that applies to the employee (such as Annual Leave Accrual):

• Use the Add exemption field to add all the unpaid leave pay items you set up in step 3.

You're now ready to pay the employee out for their unused leave.

1. Start a new pay run for the employee, and click the dropdown arrow to view their pay details.
2. Enter the hours of leave you're paying out for each unused leave pay item. For example, if they're being paid out 10 hours of unused annual leave, enter 10 hours against the Unused Annual Leave pay item.
3. Remove all other hours and amounts from the pay. Super and leave shouldn't be calculated on this pay.

You might need to change the tax amount. If that's the case, click into the PAYG field and make your changes. This ATO article might help, or ask your accounting advisor.

Then, just finish processing the pay as normal to pay the employee for their unused leave.

Now you've done the final pay, you need to enter the employee's termination date and deactivate them in MYOB Business.

You'll do this on the Payroll details tab of their employee record.

Click the Employment details tab and enter their termination date. This will delete their leave balances and standard pay details.

Click the Contact details tab and choose the Inactive employee option.

When you're done, click Save.

Finally, notify the ATO that the employee has ended their employment, by adding a termination date and finalising them.

You'll do this in the Single Touch Payroll reporting centre (Payroll menu > Single Touch Payroll reporting).

Notify the ATO on the Employee terminations tab by clicking Add Termination and entering the details.

Once the employee's final pays have been accepted, finalise them on the EOFY finalisation tab. Select the employee and click Finalise and notify the ATO, then enter your details and click Send.

If you need to change something in a pay and haven't paid the affected employees yet, there are a few ways you can choose to handle it:

• Make an adjustment on the employee's next pay, by increasing or decreasing the hours or amounts in any affected pay items.
• Record a new pay, adjusting only the affected pay items to cancel out the error. You'll need to zero out any pay items you're not adjusting
• Delete the pay (if you haven't reported via STP) or reverse it (if you have reported it) and re-enter it correctly. If the pay has been included in an electronic payment transaction, you'll need to delete that first.

For example, say you've underpaid an employee's wages by $50, and haven't yet paid them or reported it via STP. You can:

• underpay them the $50 in this pay, then add $50 to their wage pay item on their next pay,
• record an adjustment pay for that employee, entering $50 in their wage pay item, and making sure all other pay items are zero, or
• delete the pay and re-enter the pay correctly

If you're not sure about the right approach, talk to your accounting advisor.

If you need to fix a pay, but you've already paid the affected employees, you'll generally choose to handle this by entering an adjustment pay. You can choose to:

• Make an adjustment on the employee's next pay, by increasing or decreasing the hours or amounts in any affected pay items.
• Record a new pay, adjusting only the affected pay items to cancel out the error. You'll need to zero out any pay items you're not adjusting

If changing their pay could cause a significant financial impact for your employee, it's a good idea to talk to them about it first and agree on how to proceed. In some cases you might want to set up a payment plan, or do an out-of-cycle pay between their usual pay runs to fix the error.

If a pay run has been rejected by the ATO, you'll need to find out what caused the rejection and then fix the problem.

To find what caused the rejection, go to the Payroll menu > Single Touch Payroll reporting > STP reports tab, then click the Pay period dates for the rejected report. You'll see information about the error, along with an error code.

Next, click here to look up the error code and find out how to fix it.

After fixing the issue, the report will still have a rejected status, but the updated payroll information will be sent to the ATO the next time you process a pay run or send an update event.

If an STP report has a status of Accepted with errors, it means that the ATO has accepted your report but you'll need to fix some of your employee's details before your next pay run.

To see what you need to fix, click on the Accepted with errors status. In the report details, you'll see the things that need to be fixed (for example, an invalid tax file number). Edit the employee's details to fix the errors.

The next time you do a pay run, the year-to-date figures for these employees will be sent to the ATO.

Learn more >

Sometimes there can be a delay between your STP reports reaching the ATO and being displayed on the ATO business portal. If all your STP reports have a status of 'accepted', they should appear in the portal.

If they still don't match, try sending an update event. If you're on STP Phase 1, record a $0 pay for all employees, and if you're on STP Phase 2, click the Send update event button in the Payroll reporting centre.

If that doesn't fix the problem and your STP reports still don't match the ATO business portal, you can contact the ATO.

Sometimes, STP reports will have a status of Sending until the ATO receives them. This can take up to 72 hours during peak periods.

There's nothing to fix. The report's status will be updated once it's received by the ATO.

Employees might be missing from your STP reports if their Employment basis is set to Other (Not Reportable). You can change this on the Payroll details tab of their employee record (Payroll menu > Employees).

If an employee is missing from the EOFY Finalisation list, make sure you've included them in at least one pay during the current financial year, after you set up STP.

If they're still not showing up, try recording a $0 pay for the employee (STP Phase 1) or doing an update event (STP Phase 2).

Once you've declared and sent the employee's year-to-date amounts to the ATO, the employee will appear in the finalisation list.

Each type of leave has:

• one leave accrual pay item (which looks after the amount of leave being accrued), and
• one linked wage pay item (to look after the amount being paid when leave is taken)

These pay items are linked together - for example, the Annual Leave Accrual pay item might be linked to the Annual Leave Pay wage pay item.

If you've got two or more leave accrual pay items linked to the same wage pay item, you'll get this error when you try to pay leave.

To fix this error, go to the employee record for the employee named in the error message. In the Payroll details > Leave tab, click on each leave accrual pay item, and check the Linked wage pay item. Make sure each accrual pay item is linked to a different wage pay item.

If a wage pay item has been used more than once, click the x icon to remove it, and click Add linked wages to add a different one that hasn't been used elsewhere.

See more about setting up leave >

This error can occur if the RFBA amount you're reporting is below the ATO's threshold (currently $3,773 in 2022). Make sure the combined value of an employee's RFBA is above the  thresholds set by the ATO.

If unsure what to report, check with your accounting advisor or the ATO. 

See more about reportable fringe benefit amounts >

If a payment has a status of Errors in the payment portal, click the payment to view the error message for information on what caused the error.

If you can't fix the issue in the payment that caused the error, you'll need to send an email to payments_support@myob.com or contacting our support team via Live Chat.

If a payment on the Super payments is showing a status of Payment Failed or Reversal Required, or is taking a long time to complete, here's what you need to do:

• Payment failed - There was an error making this payment, and you'll need to contact product support .
• Reversal required - There was an error which prevented the contributions being paid into your employees' superannuation funds. MYOB will transfer the funds back into your bank account. You'll need to reverse the payment and record it again.
• Processing payment - If this status is showing for more than 5 days, contact us   to look into it.