The temple complex has shrines for Lord Aiyappa and Mother Durga.

Devotees pray to Lord Ganapathi to have all their wishes realized.

During the year 1795, the capital of Travancore Samasthan was shifted from Padmanabapuram to Thiruvananthapuram.  King Rama Varma sent majority of his security men to the new capital who carried with them the idol of Ganapathi.  This was originally installed in the old Srikandeswaram temple.  The security men requested the Maharaja to install the idol in Kizhakku Kottai for their worship.  Accepting their request, King Ayilyam Tirunal built this new temple installing the idol of the same Lord Ganapathi.  During the temple hours, a minimum of 25,000 coconuts are broken in the shrine and sold in auction.  The bidder helps devotees break the coconuts here and take them himself.  There is a stiff competition to succeed in the auction bid.

About 250 years ago, during the rule of kings, security men were posted on the four sides of Padmanabapuram fort.  There was a temple for Yakshi (Mohini) who was ever furious.  The place was also hilly and dense with tamarind trees.  Only those with high will power and courage can stand in this place.  Many of them would be found lying fainted in the next morning.  Many were doing the job simply due to their fate.  A new man was posted for the job.  A staunch Vinayaka devotee, he was ready for the job.  He had a happy bath in the Valliyur river before going for the job.  Something hit his leg.  He found a small 6 inch Vinayaka idol, put it in his bag and proceeded.  Yakshi began her attack on him but could not go near the new security as Lord Vinayaka would not allow her.  Next morning, those who came for the next shift were surprised that the man was safe, afresh and healthy.  He showed them the Vinayaka he had with him and said that Vinayaka was the security to him during the night.  They built a temple there and installed Lord Maha Ganapathi and named Him Military Ganapathi.