Puna clavarioides grows in high-altitude steppes and monte shrublands in an extremely arid environment. It is found well camouflaged on rocks and sands among scattered shrubs or grasses, but often in barren places where no other kind of vegetation can survive.
There are several roads crossing its range. Current and projected mining activities, as well as tourism are also threatening the species.
Extraction by collectors is considered low risk, as it is difficult to find and occurs in areas of difficult access.