Scalan was a small, clandestine community set up in the 18th century in the Braes of Glenlivet at a time when the religion was illegal.
The planning committee of the Cairngorms National Park Authority (CNPA) has now granted planning permission to Crown Estate Scotland to carry out a variety of works at the site.
These include the restoration and repair of the north and south mill buildings, bringing a timber waterwheel back into working order and creating new access paths.
Planning officer Stephanie Wade said: “The proposed works look to help preserve the historic fabric and integrity of the mill buildings while giving members of the public greater accessibility to the site.
“It is very much supported by both Historic Environment Scotland and the Architectural Heritage Society of Scotland and the plans meet with our own policies around the reuse of old buildings and our support for cultural heritage projects.”
Peter Argyle, planning committee vice-convener, said: “I am delighted to support this application, with Scalan being so historically and culturally significant.
“Making the site safe and easier to access will result in this hidden gem being a must see for visitors to the area.”
The Roman Catholic seminary was originally built in 1767 in the guise of a farmhouse, with mill buildings added in the late 19th and early 20th century.
These are considered to be of significant importance in terms of the historical, social and agricultural development of Scalan from the 18th century to the early 20th century.
The north mill, which houses a very rare threshing machine, believed to be the oldest surviving one in situ in Scotland, will have both external and internal renovations.
This includes the restoration of the timber waterwheel, which alongside the reinstatement of the north lade will allow for manned demonstrations for visitors.
Historic graffiti from as far back at 1874 will also be preserved.
Similarly, the south mill will be sympathetically restored, but its iron waterwheel will be for display only.