Phu Gon, or Pu Gon Dechen Choeling, is a monastery founded by Kunkhyen Dolpo Sangye. It is located in Dolpo Pentsang Midak Jñana Yeshe, or Yeshe Wangchuk Tsang's field, Tartang Ringmo, near Kayo Ri, and has a history of about 700 years. In Phu Gon Dechen Chöling, there is a small stupa called Je Nyi's statue or Yong Drak Kuduk Chorten. According to local legend, it was built by Je Nyi himself, the same height as Kunkhyen Dolpo Sangye's statue, and it still exists today. Similarly, inside the assembly hall, there are some treasure vases made by Kunkhyen Dolpo Sangye himself. Although this monastery was in ruins for many years, Karma Lhundrup, the uncle of Komang Tulku, who was both a tantric practitioner and a doctor, renovated it twenty years ago and built a small assembly hall and some monks' quarters. After his death, Komang Tulku Rinpoche took care of it, and in 2013, the esteemed Tulku Rinpoche Tashi Gyaltsen Pal Sangpo, who is known as the reincarnation of Jetzun Taranatha's activities, and many other lamas and Tulkus were invited to visit. The local lamas and monastic communities offered the monastery to him, which he accepted, and named it Jonang Puk Monastery Dechen Chosling, and performed a three-day Kalachakra Puja. He gave Kalachakra empowerment, longevity empowerment, and profound teachings to the entire monastic and lay community of upper and lower Deppa, and a deep connection of Dharma and Samaya was established between them.

Jonang Ngeton Takten Shedrup Choekhor Ling was founded in 1716 (12th Fire Monkey year) by Tsangpa Ngawang Tenzin, a representative of the powerful yogi Chalongpa Ngawang Trinley Namgyal. This monastery focuses on the Six-Limbed Yoga of the Completion Stage and the study of the Five Great Texts of the Jonang tradition. The Nepal Jonang Ngeton Takten Shedrup Choekhor Ling was re-established in 2005 near the Boudhanath Stupa in Nepal by Jetsun Tara Nath's reincarnation, Chogtrul Tashi Gyaltsen, in accordance with His Holiness the Dalai Lama's advice. This was done to serve as a center for the general Buddhist teachings and especially for the glorious Jonang tradition. Initially, it provided educational opportunities for young children from areas within Nepal that lacked adequate educational resources, including Karmarong, Yolmo, Dolpo, and other Monpa regions. Later, in 2013, the monastery was relocated to Leshö and expanded. It now includes a main assembly hall, teaching courtyard, monks' quarters, and other complete facilities. Currently, there are 255 monks who diligently study the five major texts of the Gyalwa Jonang tradition, as well as common sciences and the three activities of teaching, practice, and work. In 2017, a new tantric college was constructed, where over a hundred students are currently pursuing studies in Buddhist culture. In 2024, after more than eighteen years of completing studies in the five major texts and common sciences, the title of "Kachupa Geshe" (Ten Thousand Verses Scholar) was conferred upon eleven monks.

The Jonang Tagten Damchoe Ling Ngedon Gawai Tsal was founded in 1615 in the Lhatse area of Tsang by the omniscient Venerable Tāranātha of the Wood Hare year of the 10th Rabjung. After arriving in exile, the seat of the Jonang Tagten Phuntsok Choeling was initially established in 1963 by Lama Jinpa from Rebgong in Amdo. It was named Sangye Choeling. In 1990, on His Holiness the Dalai Lama's birthday, the aged Lama Jinpa offered this monastery as a birthday gift to His Holiness. In 1997, His Holiness the Dalai Lama, while enthroning His Eminence Khelkha Jetsun dhampa rinpoche as the protector of the entire Jonang tradition, granted this monastery as the foundation of the Jonang tradition in India. The monastery's name was changed to Jonang Main Monastery, Tagten Phuntsok Choeling. In particular, the successive abbots have primarily overseen the study, practice, and activities of this monastery. In the main assembly hall, there are sacred objects including: -A self-portrait statue of the Great Buddha at Bodhgaya - A golden statue of the Omniscient Dolpo Sangye - A golden statue of Jetsun Tara Nath - A golden statue of Kalachakra - A golden statue of Protector Trakshad - A golden statue of Palden Lhamo - A golden statue of Guru Rinpoche There are also many scriptures including: - The Kangyur and Tengyur of Buddha's teachings - The collected works of the Omniscient Dolpo and his disciples - The collected works of Jetsun Tara Nath and his disciples - The collected works of non-sectarian scholars Among the spiritual objects are: - A blessed unchanging vajra that was directly consecrated by Jetsun Tara Nath - The great Jonang Tongdrol (Liberation upon Sight) and the remains of Je Yonten Zangpo There are also: - The residence of His Holiness the Dalai Lama and sacred objects within it - The residence of the supreme Kalachakra Jetsun and sacred objects within it - Many other representations of body, speech, and mind, including the co-emergent Kalachakra in the Kalachakra meditation hall. The school has five foundational Buddhist classes. The subjects studied in these classes are: Tibetan language and writing, memorization of religious practices, and English language. The debate school has fourteen classes, where the main subjects studied are: the Three Baskets of Buddhist scriptures and their commentaries, the Sutras and their explanations, and the Five Great Treatises by the Omniscient Dolpopa Sherab Gyaltsen and his spiritual heirs, as well as Venerable Tāranātha. The Kalachakra practice group has three-year duration. During this time, they primarily focus on the blessing lineage of the Jonang tradition, the Six-Limbed Yoga of Kalachakra, and also practice the profound practice of Chod on the side. Currently, there are 115 monks in residence.

The Jonang Duekhor Jortrug Gomtra Choekhor Ling was established on December 13, 2014, near Norbulingka, near Dharamsala, India, by H.E. Jonang Gyaltsab Rinpoche Dorje Lopon Khentrul Chokyi Nangwa, after seeking advice and guidance from His Holiness the Dalai Lama in November 2014. During a private audience with His Holiness On May 25, 2015, he kindly advised that it would be very good if the practice of Kalachakra Yogas, etc., could be practiced not only by Jonang but also by all religious traditions, and he also granted the name of the Duekhor Monastery as Duekhor Jortrug Gomtra Choekhor Ling. Currently, the monastic college and the philosophical college of the Dukhor Monastery are under construction, including assembly halls, monks' quarters, temples, meditation rooms, and offices. At present, this monastery of the Jonangpa tradition houses 52 monks from Tibet, Bhutan, Nepal, Ladakh, Sikkim, India, and other regions. They are diligently studying a wide range of ancient and modern knowledge, including the three levels of Prajnaparamita, the two Vinaya texts, poetry, grammar, science, computers, and art. Moreover, each year, Geshes from the Gelug school, Khenpos from the Nyingma school, and Acharyas from the Kagyu school, along with many other non-sectarian teachers, continuously practice the profound Six Yogas of the Kalachakra tradition in the retreat center. This tradition has been unbroken since our teacher, Shakyamuni Buddha, taught the Kalachakra Root Tantra in Drepung. Additionally, each year, devotees and practitioners from foreign countries, including the United States, Europe, and Taiwan, receive teachings on the preliminary practices of the Six Yogas, such as the five hundred thousand accumulations.

Jonang Trashi Choethang Monastery was initially founded by Lama Gueshe Tashi. In 2007, it was offered to Palgyalwa Jonangpa's lineage holder, Khalka Jetsun Dampa Rinpoche. This Jonang mother monastery in Monde Rang has over 40 students, and Khalka Jetsun Dampa Rinpoche has been very kind in taking care of this monastery for them. The entire administration is carried out by the Jonang mother monastery. Additionally, every year, Khenzur Rinpoche Ngawang Chokyi Nangwa from the Jonang mother monastery introduces Buddhism to the local people and bestows numerous empowerments and blessings. In addition, Lama Guepa Tashi Rinpoche holds fasting retreats in various places every year to raise public awareness of Buddhism, and is carrying out as many religious activities as possible to suit the temperament of the people. Currently, there are about 6 resident monks in this monastery.