There are some tax issued to be considered when you purchase the property in the fund:
The SMSF has to be registered for GST before settlement if the property purchased is a commercial property. The GST paid on the purchase can be claimed back from ATO by lodging quarterly Business Activity Statements.
The GST collected on the rent received on commercial property needs to be paid to ATO
Capital Gain Tax
When the mortgage is paid off and the legal title for the property passes from the custodian/bare trustee to SMSF trustee, there is no capital gain for this transfer. Therefore, there is no capital gain tax.
Stamp duty rules differ across jurisdictions. Generally, there is no stamp duty payable for the transfer of the title from bare trust to the SMSF.