Since the place was blessed by Guru Rinpoche and Tshepamey, it had come to be known as Bae Ney. However, the people mispronounced the name and so it is known as Ba Ney today. The Goenpa was founded by Lopen Damchen Rinchen.

Lopen Damchen Rinchen was originally from Kheng region. He completed his Buddhist studies in Trongsa and practiced Sangdrup Tshepamey Thro Lhamo Yidam. He had come to Trashi Yangtse on pilgrimage as well as to meet his relative who was residing there. During his travel to Trashi Yangtse, he happened to meditate on the mountain behind the old Trashi Yangtse Dzong. It is said that Bae Ney could be seen on the eastern side of the place he was meditating. He could also see a huge fire burning every night at the site of Bae Ney. One day, he went to see the place to inspect what it was that burnt every night. But when he reached there he could not find anything except the ruins of an old house. However, he found the place very peaceful; so, he built a hut and started living there. Very soon he had about ten disciples. One day, he told his disciples that he was expecting a guest. He told them to take good care of the guest. Although the disciples waited a whole day for the guest, no one turned up. However, in the night, one old Tibetan lady, carrying a bag, arrived out of nowhere. She presented the monk with one statue of Tshepamey made of sharli (east bronze). Since there was no tshe bum (long life vase) in the hand of the statue which is actually supposed to be there, the meeting of the old woman was believed to be inauspicious. It is said that he died soon after this incidence. When he was cremated, his ashes were known to have formed a small mount where his own bones had turned into Tshe-bum and was seen mounted on top of his ash hill. Later, when the monastery was built, the Tshe-bum was put inside one of the statues as inner relics.

The present-day Temple was built by one of his disciples named Tsampa Chime’s son Samten Wangchuk. Since then, his descendants had been looking after this Goenpa. However, the house was later deserted and it almost turned into ruins. One village elder appealed to H.E. Gyeltshen Trulku Rinpoche to take over the Goenpa. Considering the request, Rinpoche revived the Goenpa in 1999 by enrolling twelve monks. It was also named as Tshering Jong.

However, few years back, the Goenpa was handed over back to the village community and is now being taken care by the villagers.