According to the legend, in the early times this place was under a terrifying dacoit Kannappa. He once saw a cow loitering around the place and he caught it and decided to butcher it. But the cow somehow got free and fled. Later, he saw the same cow playing with his daughter and thus he took care of the cow from then on. When his daughter died, a Goddess came in his dream to convey that she was the one who came disguised as the cow. He thus created a shrine out of his respect for the Goddess.

The presiding deity in Chottanikkara temple is Rajarajeswari. The image of Bhagawati (Rajarajeswari) is made of laterite, and is untouched by a human sculptor. It is an irregularly-shaped image covered with a golden kavacham. This deity with four arms is worshipped as two contrasting goddesses - Saraswathi (Goddess of Knowledge) and Durga (Goddess of Annihilation). Near this image is an image of Vishnu in granite. Vishnu and Bhagawati together are referred to as Lakshminarayana.

There is also a shrine dedicated to Sastha, depicting him with his consorts Purna and Pushkala. In front of the shrine are the flagstaff and the bali peetham. To the south is a platform known as Pavizhamallithara, where the deity is believed to have appeared first. There is also a shrine for Lord Siva nearby.

On the way up to the main temple is the Keezhekkavu shrine. There is a paala tree with hundreds of nails driven into its trunk. It stands as a mark of the number of devotees having been exorcised here. People suffering from mental illnesses visit the temple, as they believe that Bhagawati cures them. The Kuruthi Pooja in the Keezhkkaavu shrine at Chottanikkara is a famous event. It is a ritual done late in the evening to invoke the goddess. Worshipping here is believed to rid devotees of evil influences, psychological ailments and evil spirits.

The Makamthozhal festival of this temple which takes place in the Kumbha month in Malayalam calendar (Feb - Mar), coincides with the full moon. It is popular among locals and devotees from outside.

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