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In the early days, the temple was under the control of five Moosad families (only there are three Moosad families still existing in modern days are Kandanath illam, Changanath illam, Vavath illam and rest of two moosad families are not existing Kizhakkillath illam and Kandangath illam) called 'Parasudayavar'. They came to be called so because it is believed that Lord Parasurama gave their right to control the temple with his axe (called parasu in Sanskrit). The eldest of the six administered and others assisted him. Whoever received this status gave up his relationship with his family and continued to reside in the temple itself. The Parasu-utayavar and 'Samudaya' appointed by the "Ooraymas"1 and "Karanmas"2 took up the administration of the temple. The Mahayogam (great conference) including the Ooraymas and the Karanmas and other representatives of the temple used to be held twice a year, one on the 'Dwadasi' before the new moon day in the month of Medam (March-April) and the other on the tenth of Karkitakam (June-July). The Parasu-utayavar was all powerful and was empowered to inflict any punishment including death sentence in the temple area. In Kali era 3493 the king Cheraman Perumal gave over the temple land to the Perumpadappuswarupam. It is seen that the Perumpadappuswarupam enlarged the area of land under the temple and entrusted the administration to the very same body, that is the 'Great conference' or 'Mahayoga'.

During those days, there were two huge Gopurams on the western and eastern sides, both seven-storied, but in clear Kerala style of architecture. Scenes from various puranas were depicted on them beautifully, and people came from many parts of the world to see them. A special kind of lamp was always kept burnt on these gopurams. It is believed that they could be clearly seen even from the peepal tree in front of Thirunavaya Temple, another famous temple on the banks of Bharathappuzha, situated 68 km from Thiruvilwamala, as there were no huge buildings then. One day, when the priests were sleeping after performing daily poojas, a person came in their dreams and told like this: 'Hey Mr., why these lamps are kept burnt here? Because, they can be seen from Thirunavaya Temple. It is auspicious to worship both temples on the same day. If you don't believe it, please go there'. The next day, the priests told their dream about parasudayavars, and they immediately went to Thirunavaya by taking a boat. After worshipping Lord Navamakunda (Vishnu), they went to the peepal tree. Then, they saw both lights burning at the eastern end (Thirunavaya is to the north-west side of Thiruvilwamala). But, on the next day, both gopurams became pierced to two by a huge thunderstorm. An Ashtamangalya Prasnam was conducted later, which proved that the Lord wants his devotees directly coming to Thiruvilwamala, and not looking from Thirunavaya. Thus, both gopurams were never renovated. Now, only basement can be seen.

Later, the temple came under the Zamorins (Samoothiri) of Kozhikode. During those days, the Ushapooja was in the name of Kollengode Valiya Thampuratti, Uchapooja on the name of the King of Kochi and Athazhapooja under the Zamorin. Many litres of Palpayasam were offered by the Zamorin. Later, the King of Kochi took the charge, after continuous revolts with the Zamorins. Once, Tipu Sultan came to attack the temple, but left the place because he knew that the place was under the control of the King of Kochi, who was close to him. Once, the Lord had many huge wealth in the form of gold coins, paddy fields and other plantations. Many of them were lost after the Land Reforms Act of 1970.

The temple had got burnt thrice. One occurred in 1827, and it was after that the golaka was made for the Lord. The next two were in 1861. After the first fire, there occurred plans to renovate the temple, but before that day, it again got burnt. The eastern sreekovil did not have any problem, and the idol was taken out of it, to get poojas. The western sreekovil got burnt completely, but the idol did not have any damage. The current temple was built in 1883 by the King of Kochi. Now, the temple is administered by Cochin Devaswom Board.

The temple is situated on the exact centre of Thiruvilwamala village, situated on the top of a hill 100 ft above the sea level. On every side except the east, there is some population. The main gate to the temple is from the west. There are more than 50 steps to reach the temple. Bharathappuzha, one of the major rivers in Kerala, flows 3 km away from the temple on the north side, and as the temple is situated on the top of a hill, the river can be clearly seen while looking downwards from the temple. On the west and east sides, there are remains of two huge gopurams, which once got destroyed under mysterious circumstances. There are two idols of Garuda, the mount of Lord Vishnu, on both sides of the main gate. There are many trees on the surroundings of the temple, providing fresh air and lush greenery to the atmosphere. Saraswathikund, the place where sage Amalaka is believed to have did his penance, is to the south of the fleet of steps on the west nada. The place got this name because there is a pit here with presence of Goddess Saraswati. There is a huge peepal tree here, and devotees write 'Om Harisree Ganapathaye Namah', the famous mantra chanted during Vidyarambham ceremony, and after that make models of many buildings arranging various stones, bricks, sand and clay. Ramanchira, a small pond, is situated near the entrance to the west nada. Devaswom rest house and cloak room are situated near them. There is no kodimaram (flag staff) in this temple. The circumbulation path is carved with stone. There are two 'aanakkottils' on both the western and eastern sides, both recently built. On the northern side, there is a large pond named 'Bhagavathichira', and there are steps proceeding to it. It is in this pond that the priests and devotees take bath before entering the temple.