About six centuries ago there was a palace at Kottarakkara which belonged to the Elayidathu Swarupam. The place got its name only after the shifting of Elayidathu Swarupam to Kilimanoor. Before that his headquarters of the Swarupam was known as Kunninemal. Here there is a Siva temple which faces to the east. It is known as Manikandeswaram temple. The main deity is Lord Siva. At the shrine Goddess Sree Parvathy faces to the west and Sree Ganapathy to the south. The temple is not much superior to other temples with regard to dignity and decorum. The gold flag staff in front of the temple has been put up only recently. The shrine where the main deity has been placed is round in shape and the roof is thatched with copper sheets. First of all devotees need to worship Lord Siva and Parvathy and then only Vigneswara, is the custom to be followed. Though the temple is actually an abode of Lord Siva, it is popularly known as a Ganapathy temple.

The idol of Vigneswara, is a magnificent one carved in wood by Perumthachan. As a part of the daily ritual smearing of oil is being carried out. As a result, the idol has been turned to black and looks as if it were a some idol. It is 3 feet high, with a small trunk and four hands, carring coir, hook, rice cake, and plantain fruit. On the neck there is a chain with beads of rudraksha and on the forehead a golden pendant. In order to get a good divine view the front portion is barred. The sub-deity Sree Dharma Sastha is located outside the main shrine.

People believe that if there take refuge for help and worship Ganapathi, they will be able to accomplish everything in life to lead a happy and prosperous life.

The annual festival of the temple is celebrated in the month of Medom (April/May). On the day of Thiruvathira the temple flag is hoisted. The festival lasts for 10 days with elaborate ceremonial offerings, grand processions with all kinds of musical instruments, and a wide variety of entertainments including Kathakali.

The favourite offering to the deity (libation) is a kind of rice cake fried in oil. The making of the cakes is to be done in front of the Ganapathy. So that he can see and enjoy the fragrance of the cake! In the past there was a special kind of offering in which the whole idol was covered with fried rice-cakes.

There is a legend behind the construction of the idol of Ganapathy in Kottarakkara temple.

It was the item when the wood-work was being carried out at the temple. Many carpenters from different parts of the state were lodged there to do the work. They competed among themselves to perform the most attractive artistic works. An old carpenter, who was among them, was a stranger and he seemed to perform his task in the most perfect manner. So everyone praised him. At night when the evening rituals were over, this carpenter ate some remnants of food offered tot eh deity and slept the temple premises.

While the carpenter was sleeping in the lonely and calm atmosphere of the temple, there occurred in this mind a beautiful form of Ganapathi. At once he stood up and looked around, but there wasn't anybody. The enchanting form of Ganapathy was still in mind. Then he decided to engrave the form on a piece of wood. To his amazement he saw a piece of root of a jack tree nearby. It is an abandoned piece of root due to its hardness. He took it and began to engrave with the help of the light coming out from fire that he made himself using small pieces of wood. He worked on it for a few hours. As a result he became so tired that he could not continue his work. Soon he fell asleep. In the morning when he woke up, he was fortunate enough to see a beautiful idol of Sree Ganapathy among his scattered tools. He bowed his bead before the idol with reverence and adoration. It is the very idol that we saw now in the main shrine. The master builder of the idol was none other than the legendary carpenter Perumthachan.