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End of payroll year

Finalise payroll and STP

These instructions are for MYOB Business in the browser. For desktop help, see the AccountRight EOPY tasks.

At the end of the payroll year (EOPY), all you need to do is finish paying your employees for the year, check your payroll data and finalise STP with the ATO.

1. Finish your pay runs for the year

Enter all pays up to 30 June and report them to the ATO. If a pay period includes dates in June and July, the date it's paid determines which payroll year it belongs to.

New to doing a pay run? Learn how to do it.

  1. Go to the Payroll menu > Create pay run.
  2. Choose the Pay cycle, pay dates and click Next.

    The Date of payment determines which payroll year the pay belongs to, even if the pay period has dates in June and July. Pays dated 30 June or earlier will be included in the finalised year.
  3. In the list of employees, select those to be paid and click Next.
  4. Review the pays and click Record. Complete the pays as normal.
    If you've finished all your pay runs, go to the next End of payroll year task.
Found something wrong in the pay? Don't worry, you can fix it.
2. Check your payroll data

There's some reports that you should run to make sure that your payroll data is accurate.

  1. Before you do the first pay in the new payroll year, make sure the Payroll register and Payroll activity reports match. Here are more details about running these reports and what to do if they don't match.

  2. And before finalising, you should also make sure the YTD verification report and Payroll summary report match. Here are more details about running these reports and what to do if they don't match.

3. Tell the ATO about terminated employees

If you terminated any employees during the year, make sure you've notified the ATO of the terminations.

  1. Go to the Payroll menu > Single Touch Payroll reporting.
  2. Click the Employee terminations tab and enter the termination details.
4. Send your payroll data to the ATO

Let the ATO know you're done for the year by finalising your Single Touch Payroll information. Do this before the ATO's deadline, which is typically 14 July.

  1. Go to the Payroll menu > Single Touch Payroll reporting.
  2. Click the EOFY finalisation tab and choose the Payroll year you're finalising.
  3. Select each employee you want to finalise and click Finalise and notify the ATO.

Once you've finalised, your employees will be able to log into my.GOV to complete their annual tax returns.

To retain your own copy of your payroll data for the year, use a report pack. This generates a set of key payroll reports for the finalised year. We recommend saving these reports as a point-in-time record of your payroll data for the whole payroll year.

Learn more about end of payroll year

Payroll tasks

  • Do a pay run
  • Manage leave
  • Report via STP
  • Pay super
  • Do a final pay

Do a pay run

When you're ready to pay employees, start a pay run by going to Payroll > Create pay run. MYOB Business will guide you through the steps, but there's a few things to know:

  • The pay cycle determines which employees you'll be paying. You'll only see employees whose pay cycle matches the one you choose for the pay run.
  • When you're entering pays, expand each employee in the list. You'll see all the pay items assigned to them, which cover all the different parts of the pay, including wages, allowances, leave, super and tax. You can override the default hours or amount against a pay item to change what you're paying the employee, or to enter leave they're taking.
  • When you're done, just click Record and send your employees their pay slips.
  • Next, you'll report the pay to the ATO via Single Touch Payroll.
  • Finally, all that's left is to pay your employees what they've earned.

Manage leave

Manage each employee's leave accruals and balances on the Leave tab of their employee record. Use leave accrual pay items to set up the types of leave they're entitled to, and enter any carry over leave balances owing to them. If you're not sure what an employee is entitled to, the FairWork website is a good place to start.

When you pay leave, you'll use a wage pay item linked to a leave accrual pay item. This lets you handle the payment and accrual of leave at the same time when you do a pay run.

Here's some common things you might want to do when managing employees' leave:

Learn more about setting up leave and managing leave in MYOB Business > 


Report via STP

Single Touch Payroll (STP) is a simple way to report your employees’ payroll information to the ATO and keep your business compliant. It’s included with your MYOB subscription, so there's no additional charges.

Once you're set up, you'll send your employees' salary, tax and super info to the ATO each time you finish a pay run. This means end-of-year reporting is a breeze and your employees can access their up to date payroll information through the ATO's online service,  MyGov .

Find out how to:

Pay super

Before you start, set up your employees' super funds in MYOB Business and sign up for Pay Super, so you can easily pay each employees' super contributions into their funds directly from your software.

In MYOB Business, superannuation is calculated and tracked using pay items. We've started you off with a default set of pay items to handle different types of super contributions, including a Superannuation Guarantee pay item that you can set up to keep up with the mandatory minimum rate required by the government. You can add any more superannuation pay items you need.

Once you've assigned any applicable superannuation pay items to each employee, superannuation will be calculated and accrued when you pay them, based on the rules in the pay item.

Each quarter, use Pay Super to pay your employees' super contributions to their super funds.

Super not calculating correctly? See how to check and adjust superannuation.

What goes into a final pay?

When an employee leaves your business, you'll need to process their final pay. This will include their regular pay (up to their last day of work) and their unused annual leave.

Depending on the employee's workplace agreement and their reason for leaving, there may also be other payments you’ll need to finalise, like:

  • unused long service leave
  • redundancy
  • an employment termination payment (ETP), for certain payments including redundancies or pay in lieu of notice. ETPs should be processed before you do the employee's final pay.
    To find out if a payment is defined as an ETP, check the ATO website .

You'll also need to report the employee's termination to the ATO via STP.

Some useful resources

To learn about tax on final pays, see this ATO information.

For the rules, calculators and other final pay resources, check the Fair Work website.

Process a final pay

Final pays can get complicated so we recommend you speak to an accounting advisor about the specifics of your final pay.

Before you do the final pay, make sure you've processed any ETPs that are required for the employee's circumstances.

1. Process the employee's last normal pay

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.

2. Find out how much unused leave to pay them for

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.

3. Set up pay items for unused leave

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.

4. Make sure super and leave aren't accrued when you pay the unused 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.


Can't click Add exemption? This means the superannuation or leave accrual pay item isn't set up to calculate as a percentage of wages. In this case, you'll need to manually remove the superannuation or leave amount when you pay the unused leave.

5. Pay the unused leave

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.

6. Deactivate the employee and record their finish date

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.

If you're reporting to the ATO via STP Phase 2, you'll no longer need to provide an Employment Separation Certificate. Otherwise, visit the Department of Human Services website for details.

7. Report the termination to the ATO

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.

Payroll errors and issues

  • Fix a pay
  • I'm getting an error
  • Adjust leave accruals
  • Returned super contributions
  • Check if a pay is correct

Fix a pay

Need to fix something in a pay run? The way you handle it depends on what needs fixing, and where you are in the process of paying the money to your employees and reporting the pay via STP.

Already reported the pay via STP? When you report via STP, you're sending each employee's year-to-date totals. So once you fix the error, either by reversing and re-entering the pay, or adjusting it in a later pay, the next time you report via STP, the ATO will get the correct, updated totals.

I haven't paid the employee

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.

I've paid the employee

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.

STP errors and issues

My STP report was rejected by the ATO

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.

MY STP report was accepted with errors

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 >

MY STP reports don't match the ATO business portal

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.

The ATO hasn't accepted my report yet

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.

An employee isn't showing up in STP reports

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.

Payroll errors and issues

I'm getting an error about a wage pay item being linked to more than one leave accrual

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 >

I'm getting an error when entering reportable fringe benefit amounts (RFBA)

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 >

I'm getting an error when I try to pay an employee directly into their bank account

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  contact us .

I'm getting an error when I try to make a super payment

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 us.
  • 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.

What if a super fund advises that they didn't receive a payment?

It usually takes around four business days for superannuation payments to be authorised, processed and received by super funds. However, delays can occur (such as payments being rejected due to data errors), so we recommend allowing up to 10 business days for your payment to process. If your payment hasn't been received after 10 business days, please contact us.

Adjust leave accruals

You can check an employee's leave balances in the Leave balance report. If the amount of leave accrued is wrong, you can fix it by doing a pay run where all the hours and amounts are set to zero, and you only adjust the leave accrual pay item. See Managing your employees’ leave .

There's a few other types of adjustments you might need to make:

An employee was paid for leave but didn't use it

If an employee was paid for leave but didn't end up taking it, you can give them back their accrued hours in their next pay run. You do this in exactly the same way as when you pay leave, except you'll enter the number of leave hours as a negative against the applicable leave wage pay item. Depending on your setup, this will increase their Base Hourly or Base Salary amount automatically. Otherwise, you'll need to increase this value by the amount they were paid for the leave.

This means their net pay won't change, but their leave balance will be fixed and the values will be reported correctly to the ATO.

If they were also paid leave loading, this means they were overpaid. You'll need to fix this by entering the number of hours leave loading they were paid as a negative number in the leave loading wage pay item. This will reduce their total pay.

Here's some more details.

Change annual leave to sick leave

If an employee got sick while on annual leave and wants to change their leave type, you can do this in the next pay run.

Enter the number of hours of annual leave they want to change as:

  • a negative number against the annual leave wage pay item
  • a positive number against the personal leave wage pay item

For example, if they took an 8 hour day as annual leave and want to change it to sick leave, you'd enter -8 in the annual leave wage pay item, and 8 in the personal leave wage pay item.

This won't change their total pay, but will fix their leave balances to reflect the leave they've actually taken.

Here's some more details .

Handling returned super contributions

If you've received an email from the Pay Super Team, it will tell you why you need to reverse and reprocess a super payment. For example, you might need to fix employee or super fund details.

You'll also need to reflect what's happened in MYOB. To do this, first, use a Receive money transaction to record the returned super amount.

Next, record a pay to reverse the super. Enter the value of the returned super as a negative number in the Superannuation Guarantee field, and zero out all other amounts and hours.

Finally, once you've fixed the problem, reprocess the super payment. Record a new pay with the super amount as a positive number in the Superannuation Guarantee field, and zero out all other amounts and hours. You can then pay the contribution to the fund as usual.

Here's all the details.



Check if a pay is correct

The amounts in your employees' pays are calculated based on the information that was entered when they were set up in MYOB. As long as these details are correct, the tax and super amounts will always calculate according to the ATO's rules. Another thing to consider is how your pay items are set up and who they are assigned to .

In a nutshell – once you're set up, all the hard work is done and pay day should be a breeze.

If you're not sure if an employee's details are correct, it's a good idea to talk to the employee. You can also check their setup in MYOB via Payroll > Employees > click the employee's name.

If you want to confirm that a pay is correct, here's a few things you can check:

If you've made a payroll mistake, see how easy it is to fix.


Where do I find the year-to-date balances I've paid my employees?

The best place to find the year-to-date (YTD) amounts you've paid your employees is the Payroll register or Payroll activity reports (Reporting menu > Reports > Payroll tab).

You can also see an employee's YTD pay history in their contact record (Payroll menu > Employees > click an employee's name > Payroll details tab > Pay history tab).


Where's the payroll information on pay slips coming from?

Here's a breakdown of what you'll see on a typical pay slip and where that info comes from.

  • Your business name and ABN are taken from your business settings (click your business name > Business settings)
  • The Annual salary and Hourly rate come from the employee's contact record (Payroll menu > Employees > click the employee's name > Payroll details tab > Salary and wages tab)
  • The Payment date and Pay Period From and To dates are specified when you do the pay run
  • The employee's Superannuation Fund is set in their contact record ( Payroll menu > Employees > click the employee's name > Payroll details tab > Superannuation tab)
  • The Memo/payslip message can be entered when you do the pay run
  • The pay items listed at the bottom of the pay slip are the ones you've assigned to the employee, like Base Hourly, Base Salary, allowances and deductions.

Personalise your pay slips

Add your own touches to the pay slip by adding your business logo by clicking your business name > Business settings > Brand settings tab. You can also customise the emails you send your employees on pay day by clicking your business name > Payroll settings > Pay slip email defaults.

Get started with payroll

  • How does payroll work?
  • Set up your employees
  • Do your first pay run

Key points

  • First set up your employees. Use self-onboarding to make it easy for everyone.
  • Choose what to include in pay runs. Set up pay items to cover things like wages, allowances, leave and super and customise for each employee.
  • Pay cycles determine which employees are included in a pay run.
  • When you do a pay run, you can add leave or adjust hours and amounts in an employees pay.
  • You can make super payments and report via STP directly from your software


Set up your employees


Do your first pay run


Payroll FAQs

Where do I find my pay slips?

Each time you do a pay run, you'll be able to view and send pay slips after recording it.

If you're looking for pay slips from a past pay run, go to the Payroll menu > Pay runs and click on a pay run. Click View PDF to see the pay slip for each employee in that pay run.

Can I customise pay slips?

You can upload your business logo to show on your pay slips by clicking your business name > Business settings > Brand settings. You can also add your own touches to the pay slip emails you send your employees. Just click your business name >  Payroll settings  >  Pay slip email defaults .

Where can I find more information about my payroll limits and fees?

 To learn about how your subscription handles payroll fees and limits, see this help topic.

Can I send an employee's TFN declaration to the ATO through MYOB Business?

If you're asking new employees to enter their own details using self-onboarding, there's no longer any need to get them to fill in a paper TFN declaration form, and all their details will be sent to the ATO automatically.

If you're adding employees by entering all the details yourself, you'll still need to get a paper Tax File Number declaration form from them and send it to the ATO.

More resources

  • Payroll obligations and compliance

Know the rules to meet your obligations


There's been a legislation change and I don't know what it means

Most changes that affect your payroll come from the ATO. They make the rules and we update our software to help you stay compliant.

When there's a legislation change, like updated tax tables for a new payroll year, we'll build this into your MYOB. This means you don't have to worry about it.

If you want more information about a specific legislation change that impacts your payroll, we'll typically provide help content for it. You can search our help at

If you're not sure how a legislation change impacts your business, we recommend speaking to an accounting advisor. Or go straight to the source and contact the ATO, or search their website.

How do I stay on top of superannuation rate changes

There's a setting in MYOB that takes care of this for you. The Superannuation Guarantee pay item looks after your employees' super guarantee contributions, and it controls how they're calculated.

If the Calculation basis is set to Minimum required rate, you can relax knowing your employee's super will always be calculated at the current, correct rate.

Learn more about staying compliant with super guarantee rate increases.

How do I know if I'm complying with the ATO's requirements for STP?

When you set up STP in MYOB, all your payroll details are checked to make sure they meet the ATO's requirements. If anything is wrong or missing, you'll be advised so you can fix it.

Once you're set up, the payroll details are checked each time you do a pay run – just in case you've added or changed anything.

Sending your payroll details to the ATO is just part of running your business. MYOB makes it easy to stay compliant by making sure your payroll information is complete and in the right format.



Still need help with payroll?

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