The uniqueness of this temple is the equal importance given to both the Main prathishtas Lord Maha Vishnu and Lord Ayyappa. The temple has Dwaja Prathishta which was done simultaneously with the main prathishtas. The other prathishtas are Lord Ganesha, Lord Murugan, Shree Bhadrakali, Nagadevas and Navagrahas.
In addition to above, there is a prathishta of Yogeeswaran – in memory of a sage who was worshipping Lord Mahavishnu at the present temple site centuries ago. (This astonishing fact came to light during Ashtamangalya Prashna - the ceremony held for reviewing planetary positions of the temple land. In the close proximity of this temple, there are temples of Lord Shiva and Lord Maruthi (Hanuman) also.