Romans Cottage, Adams Cottage and Granny's Cottage are all registered by the New Zealand Historic Places Trust as category 2 protected buildings and date back to the 1800s.
In February 2007, Mr Cleary was accused of destroying the cottages by "wilful neglect" before the Queenstown Lakes District Council struck a $1.9 million deal with Lake Hayes property developer John Martin.
Mr Martin bought the cottages from Mr Cleary and then sold them to the council.
The council then set up the Arrowtown Trust to oversee the restoration of the cottages.
The trust, which has been working on the restoration of the three cottages, has applied for resource consent to change the use of two of the cottages.
The application, which has been publicly notified, seeks to use Romans Cottage, at 65 Buckingham St, for a cafe/artist gallery, operating seven days a week from 9am to 9.30pm, with all staff vacating the site by 10pm.
It also seeks to use Adams Cottage, at 61 Buckingham St, to house "professional offices".
The use of the Granny Jones Cottage, at 59 Buckingham St, would continue to be used in a commercial capacity.
Consent was also sought for landscaping of the three sites housing the cottages, to create a garden space for anoutdoor area of the cafe "with the potential to also be used for small-scale market days".
"The overall intention is to enable high-end boutique commercial activities, as well as office use within these cottages."
The application said the proposed commercial uses would provide a "practical and appropriate use" of the buildings and ensure their long-term viability.
It also said public access to the cottages would allow people to experience the cottages and their surrounds "enabling them to make a valuable contribution to the knowledge of New Zealand's past", while "enhancing the general appreciation of heritage sites".
> Submissions on the Arrowtown Trust's application close on July 5.
