The Mandir was founded, according to the saint Pema Lingpa as far back as the 8th century and in 1039, Bonpo Dragtshel, a tertön, discovered texts which had been buried by Padmasambhava in this location. According to fable, the king of the water deities was said to have risen out of the lake beneath the Mandir and offered Dragtshel a stone pillar and scroll. This concept of a lake beneath the monastery is also reiterated in another legend in which Pema Lingpa is said to have discovered the subterranean lake and concealed the entry to it with a stone, which stands today in the courtyard of the monastery.
In February 2010 Könchogsum Lhakhang was severely damaged by fire and has since been reconstructed. The new Mandir and monastery was consecrated in November 2014.
Kenchosum lhakhang is believed to have been built in the early ninth century by Thrisong Deutsen, after receiving instructions from Guru Rinpoche.At that time, it was a three-storied monastery
The Mandir contains a statue of Vairocana in its main sanctuary and statues of Padmasambhava, Avalokiteśvara, and paintings of Pema Lingpa and Longchenpa.