The place that we now call Mahaganapathy temple is actually Kizhakkekara Siva Temple. The main deity is none other than Lord Siva himself – Siva facing eastward. In fact Ganapathy is only a minor deity here. But the temple today is famous as a Ganapathy temple rather than a Siva temple.
The legend behind this is that Kizhakkekara temple was the property of two Nampoothiri houses – Akavoor and Oomanpally. Padinjattinkara Siva temple belonged to the royal house of Elayidathu.
One day, before sunrise, rituals were taking place for the consecration of Siva at the Pandinjattinkara temple, the work of which was managed by the legendary Uliyannor Perumthachan. Outside the temple , while listening to the manthras , he started chiselling a piece of jackfruit tree. To his surprise, he found that it was the form of ‘Ganapathy’ that was taking shape. Thus he asked the chief priest to enshrine ‘Ganapathy’ also after the consecration of Siva. The chief priest denied. "This is a Siva temple. Ganapathy cannot be consecrated here."
Perumthachan, desperate, walked towards the east and thus reached Kizhakkekkara Siva temple. As that priest was preparing offerings for the lord- Unniyappam. Perumthachan asked him " Can you not sanctify this Ganapathy here ?". The priest agreed. Perumthachan viewed the place- Siva facing east, in front of that it is Ganga, Parvathy turned towards the west. Southwest there is Sastha and northwest Subrahmanya. If Ganapathy too is installed, Siva family will be complete. The place will be none other that Kailas itself. Thus Ganapathy was installed southeast by Perumthachan.
Perumthachan then asked the priest " Unni Ganapathy must be hungry.What is the sacrificial food that you have prepared?".
"Unniyappam" was the reply. On a leaf, the priest placed six to seven Unniyappams stringed together. Perumthachan, with all his heart devoted his first offerings-Koottappam. Koottappam is still known to be the most wanted nivedhyam for Kottarakkara Ganapathy.
After the offering Perumthachan affectionately declared "Though father is the main diety, the son will be much more famous". His words proved to be true. Kizhakkekkara Siva temple is now known as Kottarakkara Ganapathy temple.