Founded by monks from Sopara in the 1st century BCE, the monastery flourished till the 10th century CE. Later it continued to exist, albeit on a small scale till the 16th century. It served as a religious center for several centuries surrounded by other monastic settlements. Kanheri was surrounded by numerous trade centers and port cities linked to the Silk route in central Asia. The inscriptions at Kanheri provide details of patrons received by the monastery. It mentions names of Kings, their family members, ministers, administrative officers, traders, monks and nuns who have given extensive donations to the monastery at Kanheri. The donations were made to excavate caves, built temples, create reservoirs and water cisterns in the form of money. Some inscriptions indicate the monastery had received land grants and fixed deposits as donations.

Among the significant caves at Kanheri cave number 2, 3, 11, 34, 41, 67, 87, and 90 are considered as must-visits. Cave 3 is the main chaitya (Buddhist Prayer Hall) at the site. Cave 11 is a unique cave used for rituals in Mahayana Buddhism and has no parallel other than cave number 5 at Ellora. Cave 34 displays the 6th-century murals, while cave 67 is a sculpture gallery filled with various sculptural panels of Buddhist deities. Cave 41 has the oldest known image in the world of Bodhisattva Eleven Headed Avalokiteshwara. Cave 87 houses more than 60 brick stupas erected in the memory of various teachers who once lived at Kanheri. Cave 90 has sculptural masterpieces engraved in it. A pair of Japanese inscriptions and three Pahlavi inscriptions of Zoroastrians makes this cave a worth visiting place. Xuan Zang, the well-known Chinese Buddhist monk, had visited the caves at Kanheri in the seventh century CE. References to Kanheri appear in the various ancient literary traditions from Asian countries like Nepal and Tibet.