The Meditation Centers and Temples are scattered all across the hillside. Phajoding is a large monastic complex with ten temples and fifteen monastic residences, many of which are used for extended meditation retreats. Phajoding takes its name from the saint Phajo Drugom Zhigpo, who meditated there in the 13th century during which he had a vision of Chenrizig - the Buddha of compassion. It is therefore considered to be one of the most sacred meditational sites in Bhutan. Most of the buildings at Phajoding were constructed in 1748 by Gyelwa Shakya Rinchen (who is considered to be the reincarnation of Rechungpa, the heart disciple of Milarepa) the Ninth Je Khenpo, whose image is the central figure in the main temple.
Though at one time regarded as the most prosperous and affluent monastery in Bhutan, its affluent status declined over time due to negligence by the Central Administration. The regrettable turn of events could likely have been the reason as to why Phajoding Monastery was listed among the five most Endangered Cultural Monuments by the World Monuments Fund in 2010.