Sri Embar, the venerated preceptor is closely associated with the ancient village of Madhuratnangalam and the Sri Vaikuntha Perumal Temple there. Hence Sri Embar is found to have a great share in the legendry story associated with Sri Vaikuntha Perumal temple. Sri Embar, who is believed to be an incarnation of Pakshiraja or Garuda (Garudaamsham), was the first cousin of the pre-eminent Srivaishnava Acharya, Ramanuja. According to the traditional legendary accounts this ancient preceptor lived for 110 years. Sri Embar, whose original name was Govinda Bhatta, was initially a student of Yadavaprakasa in Tirupputkuzhi, near Kanchipuram, along with Ramanuja.

When Govinda found out that their teacher, following differences with Ramanuja, was planning to kill him, he advised his cousin to escape to safety. Govinda accompanied Yadavaprakasha on a pilgrimage to the north, and according to traditional accounts, while bathing in the Ganga, a linga appeared in his hand. After this incident he came down south, and started living at Kalahasti, worshipping the linga before Periya Tirumalai Nambi, at Ramanuja`s behest and brought him into the Vaishnava fold. He became Ramanuja`s ardent and faithful student and later took to asceticism (sanyasa). He was given the name Embar by Ramanuja, which was a part of the latter`s own name, Emberumanar. He was one of the seventy-four Simhasanadipatis (spiritual heads), appointed by Ramanuja to spread Srivaishnavism. Parasara Bhatta and Srirama Pillai, the two sons of Kurattazhvan (a very loyal disciple of Ramanuja) were Embar`s disciples.

Apart from this story another legendary story is also associated with the temple. As the Sthala-Purana or the legend connected with this temple depicts, Lord Vaikuntha Perumal appeared before a ruler of Tondaimandalam (comprising the region of erstwhile Chengalpattu, North Arcot and South Arcot districts) named Suparna Maharaja and blessed him. It is said that it was this king originally constructed this shrine in order to offer his veneration to Lord Vaikuntha Perumal. It was also at this sacred place that the Sapta-rishis performed Ashwamedha yoga. However the legendary stories depict that Vaikuntha Perumal Temple is not only ancient one but immensely sacred as it is the birth place of the divine preceptor of Sri Embar.