The renovation of Siva temple, as engraved in the basement of old Sreekovil of the temple, was carried out during AD 1492.

The renovation of Vishnu temple was also carried out during this period. The administration of the temple was carried out by the family of Mambattu Bhattathiri, who was also one of the trustees of Sree Poornathrayeesa temple, Tripunithura.

Bhadrakali, another upadevatha of the temple, was installed by another member of the family of Mambattu Bhattathiri, who was a loyal worshipper of Kodungalloor Bhagavathy. He used to visit Kodungalloor temple regularly. When aged, he was physically unable to visit the temple. On his last visit to the temple, he prayed to Bhagavathy that he was extremely sad that he may not be able for further visit to the temple. On that night, he dreamt Bhagavathy herself telling him that she has also accompanied him to his house and he may arrange to install Bhagavathy in the nearby temple as per rituals. Accordingly, Mambattu Bhattathiri installed Bhagavathy in the Puthankulangara temple during 1675.

Dharma Sastha, another upadevatha of the temple, was also believed to be of historical importance. It was believed that during 1790, one of the temples of North Malabar was attacked by the soldiers of Tipu Sulthan. One devotee of that temple fled with the idol of Dharma Sastha which was partly destroyed during the attack, for protecting the same from further damage. When he reached Kochi, he handed over the idol to Puthankulangara temple and it was installed in this temple near to Siva temple

Later, during the era of Sakthan Thampuran, the King of Kochi State, the temple was reconstructed during 1800. It was also told that the skin disease appeared on shoulder of the King was completely cured after praying to Lord Siva of this temple. An Oottupura was also constructed by the King for serving meals to Brahmins.

During 19th century, the administration of the temple was handed over to Muriyamangalath Mana, located near Kalady, by the King of Kochi State due to extinction of male members in Mambattu Bhattathiri’s family. The pooja and related activities of the temple was carried out by members of Tulu Brahmin family, namely Thoppil Madhom, from 1905 onwards and the contribution of this family towards up keeping the temple related activities was innumerable. The construction of the present golaka of Lord Siva and Sree Parvathy of the temple was organized by late Gopalakrishnan Embranthiri of this family.

As per the Ashtamangala Prasnam of 1990, by late Sri. Kaimukku Parameswaran Namboothiripad, the renovation of the temple was carried out during the period from 1992 to 2004 by Muriyamangalath Neelakandhan Namboothiripad, the Managing Trustee of the temple, with the guidance of Sthapathy late Sri. Vezhaparambu Parameswaran Namboothiripad and Sri. Kanippayyoor Krishnan Namboothiripad and Thanthry Sri. Puliyannoor Sasi Namboothiripad. The punaprathishta of Siva temple was carried out on 04-02-2004 (star Punartham, month Makaram). The pooja and other related activities were rescheduled after the renovation of 2004 by Thanthry. The six day long Ulsavam of the temple was also scheduled for the month Makaram with Aarattu day as Punartham, which eventually coincides with Punaprathishta Dinam. The importance of Lord Vishnu is as equal as that of Lord Siva and the Vishnu temple was also renovated during 1992 to 2004 and the punaprathishta was done on 04-02-2004.

The dhyanam of Bhagavathy of the temple is exactly as that of Bhadrakali of Kodungalloor temple. Kalamezhuthu Pattu carried out by persons from Kurup category during the Mandalam period starting from 1st day of Vrischikam every year is a traditional offering to please Bhagavathy. This event was restarted during 1986 and still continuing in the temple. The prathishta of Arukola, a devotee of Bhadrakali, situated near to the temple, was renovated during 2001. Thalappoli procession for Bhagavathy is being carried out from Arukola prathishta to the temple on Meenabharani day every year. Idol of Vethalam, who is considered to be the vehicle of Bhadrakali, was also installed by Mambattu Bhattathiri. This prathishta was also renovated during 2004.

The idol of Dharma Sastha was renewed as per the astrological verdict of 1990 and the installation of new idol was carried out on 04-02-2004. Makaravilakku celebration has been carried out at Dharma Sastha temple every year by the Velar Service Society for last many decades. Other deities such as Ganapathy, Namaskaramandapa Yakshi, Nagarajavu and Nagayakshi were also renovated and the punaprathishta was done during 2004.

Based on the Devaprasnam of April 2006, Dhwaja prathishta of Siva temple was carried out on 10-04-2008 (star Rohini, month Meenam). The teakwood procured from Thodupuzha Forest Range for the dhwajam was transported from the forest to the temple premises in a trailer and this procession was considered to be one of the first historic events of its kind among the temples of Tripunithura region. Rajappan Achari was entrusted to supervise the renovation of the temple and construction of the dhwajam. His dedication and experience in this field was highly appreciable which in turn resulted for timely completion of the projects. The renovation of Bhagavathy temple was started during 2011. After completion of renovation, Punaprathishta was carried out on 14-07-2013 (star Uthram, month Midhunam).

Another peculiarity of this temple is a large temple pond in front of the Vishnu temple. The temple pond renovation project is in its initial stage. The Theerdhakkulam in front of Siva temple was renovated during 2011-2012 for the exclusive use of Melsanthi / Thanthry. Future projects of the temple are Nadappura in front of Siva temple, Alankara Gopuram, Kalyana Mandapam, beautification of temple premises etc.