Within the Gelug tradition, many of the most sensitive issues revolve around how Tsongkhapa’s legacy is to be understood and lived. One major area of debate concerns the interpretation of emptiness in the Prāsaṅgika Madhyamaka system. Gelug scholars have long discussed how to understand the scope of negation, the status of conventional truth, and whether certain readings risk sliding toward a more substantialist view. These are not casual disagreements, but detailed scholastic exchanges over texts such as the *Lamrim Chenmo* and other major commentaries, probing whether Tsongkhapa’s presentation most faithfully captures Nāgārjuna’s intent. Closely related are questions about the path structure itself, including the balance between gradual cultivation and more sudden insights, and the proper timing for engaging in highest yoga tantra relative to foundational sutra study.

Another enduring controversy centers on the practice of Dorje Shugden (Dolgyal), regarded by some as a powerful protector of a “pure” Gelug lineage and by others as a harmful, sectarian influence. Senior figures, including the present Dalai Lama, have discouraged this practice on the grounds that it fosters division within Tibetan Buddhism and undermines broader communal harmony. This has led to restrictions in many Gelug institutions, the emergence of Shugden-aligned communities, and painful fractures in what was once a more unified landscape. The controversy also touches on questions of political and spiritual authority: how far the Dalai Lama’s guidance should extend within the school, and how that relates to other traditional leadership roles such as the Ganden Tripa and monastic abbots.

Institutional and educational questions form another strand of internal debate. There are ongoing discussions about how strictly to maintain Tsongkhapa’s rigorous monastic discipline and scholastic curriculum in changing circumstances, including the place of modern subjects alongside classical philosophy. Some voices emphasize preserving intensive debate, logic, and textual study, while others stress the need to adapt for lay practitioners and new cultural contexts. Similar tensions appear around tantric practice: how prominently deity yoga and complex rituals should feature, when they should be introduced, and how much esoteric material should be made publicly accessible. These issues are often framed as a search for balance between fidelity to a demanding tradition and responsiveness to the needs of contemporary students.

Underlying many of these debates is a shared commitment to Tsongkhapa’s vision, even as its precise contours are contested. Arguments over emptiness, Buddha‑nature language, and philosophical method are not merely academic; they express differing intuitions about how best to safeguard a path that is both analytically precise and spiritually transformative. Disagreements about protectors, reincarnation recognitions, and the role of political power reveal anxieties about identity, continuity, and the integrity of transmission. In this sense, the controversies of the Gelug tradition can be seen as the outer signs of an inner effort to hold together clarity of view, purity of conduct, and skillful engagement with a complex world.