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How do I migrate payroll from another system?

Switching from Xero, MYOB or another payroll system part-way through a financial year? The Payroll software migration workflow lodges a one-off STP update so the ATO carries your employees' old year-to-date figures across to myaccountant — no duplicate Income Statements.

Do this before you finalise your first pay run in myaccountant. Once a regular pay run is finalised, the migration window closes.

Create the migration

Step 1. Go to Workflows, open the Payroll software migration card and click Create migration.

Step 2. Pick the business. One migration per business — a business with an in-progress migration opens instead of starting a new one.

Step 3. Fill in the Migration details:

  • Previous payroll software — optional; Xero, MYOB AccountRight, MYOB Essentials, QuickBooks Online, Reckon, KeyPay, Employment Hero or Other. This is never sent to the ATO.
  • Old BMS ID — required. This is your business's identifier in the old payroll system's STP setup. Click Where do I find my BMS ID? for per-system pointers (for example, in Xero it's on the Payroll → Single Touch Payroll filing screen). It must be different from your myaccountant BMS ID.

Step 4. Click Create migration. Your active employees are added automatically, starting with no opening balances.

Enter each employee's figures

Step 1. In the Employees section, click an employee's row (use Add employee for anyone missing — only active employees can be added).

Step 2. In the drawer, fill in each section — each saves independently:

  • Old Payroll ID — the employee's ID in the previous payroll system. Required for every employee, and it must be different from their myaccountant payroll ID.
  • Pay items — YTD opening balances — add each earning and deduction with its year-to-date total.
  • Year-to-date totals — Tax withheld YTD, Super contribution YTD and the super-earnings basis figure, from the previous system's latest STP report.
  • Leave opening balances — Annual leave (hours) and Personal / carer leave (hours). These are used in myaccountant only, not sent to the ATO.

Each employee's row shows a tick once their figures are complete.

Lodge with the ATO

Step 1. When the Old BMS ID is set and every employee has an Old Payroll ID and figures, the Lodge with ATO button becomes available. Click it.

Step 2. Review and accept the declaration, then send. You'll see "Lodgement queued — STP update is on its way to the ATO."

Step 3. The page checks with the ATO automatically ("Automatically checking with the ATO…"); you can also click Check ATO Status. Once accepted, the ATO links the year-to-date history from your old system to myaccountant, and the STP submission history appears on the migration.

After lodging, the migration is locked — the figures can no longer be edited. You can now run your first normal pay run; year-to-date amounts on payslips and STP will include the migrated balances. See How do I create a pay run?

Understand the concepts (Academy):

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