As usual Polonnaruwa kings too, paid their share of homage to the Kelani Vihara. Of them king Parakramabahu the Great and king Nissankamalla were prominent. The Pritidana inscription of Nissankamalla refers to Kelaniya as one of the shrines he visited in his famous tour of the religious places. He is said to have carried out extensive innovations at Kelani Vihara. He also donated large extents of lands for the upkeep of the temple and the monks.
In 1215 A.D. the South Indian invader, prince Maga of Kalinga invaded the island. He played havoc, destroyed, looted and plundered many a temple. This went on for twenty one long years. Kelaniya temple too fell in too ruins and decay. In 1230 A.D. Vijayabahu III gathered forces against Maga, defeated him and recaptured the country. He shifted his capital to Dambadeniya for security reasons