In 1193, the Nalanda University complex was sacked by Turkic Muslim invaders under Bakhtiyar Khilji; this event is seen as a milestone in the decline of Buddhism in India.

It is said that Khilji asked if there was a copy of the Koran at Nalanda before he sacked it. When the Tibetan translator Chag Lotsawa visited them in 1235, he found them damaged and looted, but still functioning with a small number of monks.

The destruction of the universities at Nalanda, as well as the destruction of many temples and monasteries throughout northern India which housed centers of learning, is considered by many historians to be responsible for the sudden demise of ancient Indian scientific thought in mathematics, astronomy, alchemy, and anatomy.

Fortified Sena monasteries along the main route of the invasion were destroyed, and being off the main route both Nalanda and Bodh Gaya survived. Many institutions off
the main route such as the Jagaddala Monastery in northern Bengal were untouched and flourishing.