Xero Integration

Connect Xero to send employer invoices, employers and payments to Xero, and mark invoices paid when Xero records the payment.

Last updated 18 Oct 2026

Xero Integration

Connect Xero and RTObase sends your employer invoices and employer details to Xero for you. When a payment is recorded against an invoice in Xero, RTObase marks the invoice paid and records the payment against each enrolment on it. You can also choose to send payments recorded in RTObase to Xero.

Access required

Choose the task you are doing. Each row is a separate action.

TaskRequired access
Open Xero settings and connect or configure XeroAdministrator

An administrator completes connection setup. Viewing sync results, raising invoices and recording payments use their own finance permissions in the corresponding sections below.

Connecting Xero

  1. Go to Settings > Xero
  2. Click Connect to Xero
  3. Sign in to Xero, choose the Xero organisation to connect, and click Allow access
  4. You return to RTObase with a green Connected badge and the Xero organisation's name

Choose one Xero organisation. Each Xero organisation can connect to one RTObase organisation.

Invoice account

After connecting, pick the Invoice account. It is the Xero revenue account for invoice lines whose course has no account of its own. Until you pick one, RTObase uses account 200, Xero's default sales account.

Account per course

A course can use its own Xero account. Open the course's details and pick a Xero account. Invoice lines and student payments for that course go to that account. Leave it on Use the invoice account to use the default. The field shows only while Xero is connected.

Tracking by site

To report income by site in Xero, pick a Xero tracking category under Tracking by site. Then match each active site to one of the category's options and click Save tracking. RTObase tags invoice lines and student payments with the site the training is delivered at. Picking a different category clears every site's option.

What syncs

  • Invoices. An employer invoice goes to Xero when you send it, including invoices RTObase creates for employer team enrolments. Draft invoices stay in RTObase.
  • Edits and cancellations. Editing an invoice that is already in Xero updates it there. Cancelling it voids it in Xero.
  • Employers. The first invoice for an employer matches them to a Xero contact by ABN, then by exact name, or creates a new contact. Later changes to the employer's name, ABN, contact or billing address update that Xero contact.
  • GST. Amounts go to Xero GST inclusive. GST-free lines use Xero's GST Free Income tax type.
  • Payments. Only the payment types you turn on under Payments below.

Invoices usually reach Xero within a minute. The invoice page shows Sending to Xero, then In Xero with a link to the invoice in Xero. The invoices list has a Xero status column too.

Payments

TaskRequired access
View invoice or payment sync resultsInvoices and payments: View
Raise invoices or record paymentsInvoices and payments: Edit

Payments recorded in Xero always mark the invoice paid in RTObase. The Payments section of Settings > Xero decides which payments recorded in RTObase also go to Xero. Nothing is sent until you turn it on.

Employer portal payments

Card payments employers make in the employer portal go to the account you pick, such as a Stripe clearing account. Choose Don't send to Xero to keep them out.

Manual employer payments

Where staff record bank transfers, cash and cheques for employer invoices. Record in Xero means staff record them in Xero and RTObase marks the invoice paid when Xero does. Record in RTObase and send to Xero means staff use Mark as Paid in RTObase and the payment goes to Xero. Pick a Manual payment account as the default. Staff can change it for each payment.

Manual student payments

Student payments recorded from now on go to Xero as Receive Money, into the bank account you pick. Each student gets one Xero contact.

Student payment income account

The income account for student payments whose course has no Xero account. Leave it on Same as the invoice account to use the invoice account.

Click Save payment settings. When a save turns on a new payment type, RTObase asks you to confirm first. Payments recorded before you turn it on are not sent. A payment Xero already has is never sent twice.

Test payments are never sent to Xero. Real manual payments are sent even while online checkout is in test mode.

Recording a manual employer payment

With Record in RTObase and send to Xero on, open the invoice and click Mark as Paid. Enter the payment date, the Xero account the money went into and a reference. Click Mark as Paid and send. RTObase records the payment against each enrolment on the invoice and sends it to Xero. Xero then shows the invoice as paid.

With Record in Xero on, an invoice that is already in Xero shows Record the payment in Xero instead of Mark as Paid.

Student payments in Xero

Each student payment reaches Xero dated in the enrolment's class location timezone, or the organisation's stored timezone when no class location is available.

The student's Payments tab shows a Xero column for payments sent to Xero. If a send fails, click the retry button next to the status. RTObase tries again within a minute.

Deleting a manual student payment that is in Xero also deletes the Receive Money in Xero. If it is reconciled in Xero, remove the reconciliation there first. Otherwise Xero refuses and RTObase keeps the payment.

Invoices with a payment in Xero

When Xero shows a payment or a credit note on an invoice, RTObase locks the invoice. You cannot edit it, cancel it or mark it paid in RTObase. The invoice page shows Xero has a payment on this invoice and the amount Xero shows. Make any change, and take the rest of the payment, in Xero.

If Xero already shows an invoice as paid and RTObase also took a payment for it, the sync fails with a warning. The employer may have paid twice, for example by bank transfer and again by card. Check both payments and refund one if needed.

A card payment refunded or disputed in Stripe after it reached Xero shows Refunded after it reached Xero. RTObase does not change Xero for refunds. Record the credit note and refund in Xero.

Student card payments made online are not sent to Xero. Connect Stripe to Xero with Xero's own Stripe feed to bring those payments and fees into Xero.

When an invoice does not sync

TaskRequired access
Retry a supported invoice syncInvoices and payments: Edit

If Xero refuses an invoice, the invoice page shows Xero sync failed and Xero's reason, such as an invalid account code. Fix the problem, then choose Retry Xero sync from the invoice's menu.

Xero will not change an invoice that already has a payment on it. Make that change in Xero, or issue a credit note in Xero instead of cancelling.

An invoice sent before you connected Xero is not sent automatically. Use Send to Xero from its menu.

Needs reconnecting

Xero stops accepting a connection if someone removes RTObase from the Xero organisation's connected apps. RTObase checks every day. When this happens:

  • Settings > Xero shows Needs reconnecting
  • Admins receive an email
  • Invoices, payments and employer changes wait, then send once you click Reconnect Xero

Reconnect to send payments

A connection made before RTObase could send payments shows a yellow banner in the Payments section. Click Reconnect Xero and allow access again. Xero then lets RTObase send payments and Receive Money.

Reconnecting keeps the Xero organisation already linked to this RTO. To switch organisations, disconnect first. If Xero returns several earlier connections without identifying your choice and this RTO has no existing tenant, RTObase asks you to remove the unwanted connections in Xero and try again. It does not choose another organisation for you.

Importing employers from Xero

  1. Go to Employers
  2. Click Import from Xero (only shown when Xero is connected)
  3. Search your Xero contacts by name, select one and click Import

You can also link or unlink an employer's Xero contact from the Xero Contact section of the employer's page.

Disconnecting

TaskRequired access
Disconnect XeroAdministrator
  1. Go to Settings > Xero
  2. Click Disconnect Xero and confirm

Invoices and payments stop sending to Xero and any waiting changes are dropped. Invoices already in Xero stay there. An invoice with a part payment in Xero stays locked in RTObase, so it cannot be edited, cancelled or paid again. Connecting a different Xero organisation later clears these locks, because RTObase forgets the old invoice links.