The Vana Durga Temple is located in the north east of the Outer quadrangle facing the west. The legend behind the structure is interesting. The Moola Vigraha was brought to Alapuzha and the installation was done with the consent of Gramadevatha namely "Mullakkal Sree Raja Rajeswary Devi". Folklore has it that Vanda Devi also expressed Her desire to serve the Vishnu Roopi Venkatachalapathy and accordingly the installation was done. VanaDurga therefore appears in three evolutes, vis Vidhya Roopi Saraswathi, Samhara Roopi Durga and Aiswarya Roopi Mahalekshmi. A unique feature is that the Nivedyam after being initially offered at the main temple is next offered here.

Apart from Thrikala pooja ,pushpanjali, Lalitha sahasranam and Lepanam are offered to Devi. Special poojas are offered during Navarathri days. Parthishta day is celebrated during the Malayalam month of 'Makaram' on 'Moolam' asterism, This synchronizes with the 41 day Mandala Maholsavam which can be called the Hindu version of Lent, the ritual observance of austerity and religious vows in connection with the Sabarimala temple festival.