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Xero

Microkeeper sends each pay run to Xero as a bill, with its wages, super and PAYG withholding against your Xero accounts. You pay the bill from your bank feed when wages go out.

Required planAll plans
Required accessSettings to connect and sync, and Report and Payroll to send pay runs

This guide covers how to:

  1. Connect an ABN to your Xero organisation.
  2. Sync your Xero accounts and tracking categories.
  3. Send a pay run to Xero.
  4. Send a pay run again.

Before you connect Xero

Connect an ABN to your Xero organisation

  1. Navigate to Menu > Settings > General > Global, then click ABN and Pay Cycles.
  2. On the ABN, click Connect to Xero.
  3. Log in to Xero and allow Microkeeper access.
  4. If your login has more than one organisation, choose it in Select Organisation and click Connect.

An ABN in ABN and Pay Cycles set to Xero, with mark 2 on its Connect to Xero button

Xero's Log in to Xero screen, with Email address and Password

The ABN then shows the organisation's name beside the Xero logo. Connect to Xero is also on the ABN's Chart of Accounts and on a pay run's 3. Export.

Each ABN connects to one Xero organisation, and stays connected until you disconnect it.

Sync your Xero accounts and tracking categories

  1. Open the ABN's Chart of Accounts, from ABN and Pay Cycles.
  2. Click the Xero button with the cog.
  3. Click Sync Accounts to bring in your Xero accounts.
  4. If you use tracking categories, click Sync Tracking.

The Xero window on the Chart of Accounts, with marks matching the steps: 3 Sync Accounts and 4 Sync Tracking, and Delete All below

Sync again whenever you add, rename or remove an account or tracking option in Xero. Xero takes up to two tracking categories on each bill line, so have only the two you use active in Xero. See Sync accounts from Xero or Reckon.

Send a pay run to Xero

  1. Navigate to Menu > Payroll > Payruns and open the pay run.
  2. Click Complete Payrun, then 3. Export.
  3. Check each line's Description, Account and tracking category, and click Save Settings if you change anything. See Map each pay run line to an account.
  4. Click Send to Xero.

Microkeeper shows Payroll data added to Xero, with a View invoice in Xero link.

The payroll bill in Xero

  • From: Microkeeper.
  • Reference: Payrun-MK-PayCycle-, then the pay cycle's ID and the pay period, such as Year 2026 - Run 49.
  • Date and Due Date: the pay run's Payment Date.
  • Amounts are tax inclusive, at each account's default tax rate.
  • It's Awaiting Payment, under Bills to pay.

When you pay wages with the ABA file, reconcile the payment in your bank feed against this bill.

Send a pay run to Xero again

To change a bill, correct the mapping or the pay run, then click Send to Xero again. Sending the same pay cycle and pay period again updates its bill rather than adding another.

Warning

Don't void a payroll bill in Xero. A voided bill can't be updated, so the next send for that pay run fails.

If Xero shows an error when you send again, for example because the bill was voided, choose v2 in the list beside Send to Xero and send again. This adds a new bill with v2 at the end of its reference. Use v3 to v5 only if the version before can't be updated either.

Xero troubleshooting

Why does sending to Xero show AuthenticationUnsuccessful or Error 403?

Disconnect Microkeeper from Xero on both sides, then connect again:

  1. In Microkeeper, open the ABN's Chart of Accounts and click Disconnect.
  2. In Xero, go to Settings > Connected Apps, and click Disconnect beside Microkeeper.
  3. Click Connect to Xero in Microkeeper and allow access again.
Why does sending to Xero show AuthorizationUnsuccessful?

The Xero login that connected Microkeeper can't create bills. In Xero, go to Settings > Users > Current Users, edit the user's permissions and turn on Expenses (Admin).

Why can't I find a Xero account in the Account list?

The list is copied from Xero when you sync. Open the Chart of Accounts, click the Xero button, then Sync Accounts.

Why does Microkeeper say Xero only accepts up to 2 tracking categories?

More than two tracking categories were synced. Make only the two you need active in Xero, then on the Chart of Accounts click the Xero button, Delete All, then Sync Tracking.

How do I connect a different Xero organisation?

Click Disconnect on the ABN's Chart of Accounts, then Connect to Xero and choose the other organisation. Sync its accounts, and check the mapping on 3. Export before you send.

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