This centuries old Shiva temple was under the direct rule of the Zamorin of Calicut. Bhaktasiromani Sundaramurthy Nayanar has written about this temple in the ancient Tamil script, Tirukova. It is one of the great temples that were destroyed during the Tipu's campaign. It is said that the devotees returned to Ambalapuzha with the idol of Guruvayoorappan just before thistemple was destroyed. Perundatta Mahadeva Temple is located on the south western side of the Guruvayur Temple.
Many stone inscriptions are found in the temple complex.Recently, excavations from the temple have uncovered evidence that the Zamorin's forces tried to defend Tipu.
When excavating the temple, two large cannons were found. The history of these two cannons dates back to the 18th century. The palace of the Zamorin Raja is located near the Perundatta temple at western side.