Since 1773,following the banning of the Church of Jesus in Portugal, the church was controlled by priests trained from the Goa Seminary. In 1858, the Diocese of Kochi was formed and Pallithura became part of Kochi as per the agreement made by Pope Pius XI with the Portuguese government. In the early19th century, with the permission of the Bishop of Kochi Diocese, Rt. Rev. Abillius, the initial work of the church was started at the place where the rocket station is located today. As a token of gratitude for saving the Dutch sailors who were travelling at sea from the stormy seas, the sandalwood effigy of Mary Magdalene was floated in many coastal areas but could not be landed anywhere. After that the effigy floated on the Pallithura beach and the parishioners tried to bring it ashore but failed.

After the parish vicar prayed and blessed, the image of Saint Mary Magdalene was brought to the ground and placed in the church. A long piece of wood with this figure washed up on the beach and the parishioners picked it up and set it up as a flagpole in front of the church. It still exists. Based on the above developments, the church was renamed as Saint Mary Magdalene. In 1933, Rt.Rev. Abillus, the Bishop of Kochi, appointed Father Peter Puthanpurakkal from Kochi as the first vicar of the Church of Saint Mary Magdalene in Pallithura. In 1962, this soil witnessed the historic moment that gave wings to India's space dreams through the remarkable intervention of His Holiness Peter Barnard, who was the Auxiliary Bishop of Thiruvananthapuram Diocese.

It was sheer patriotism and unsullied obedience to their spiritual forefathers that impelled the honourable older generation of this country to unconditionally dedicate their homes, their land where the temple and the school is located. In 1963, in the second phase temples and ancestral cemeteries to the land of their birth, were given away for the establishment of the International Space Research Organization (ISRO). The land from Cherumankara to the place of the church, cemetery and Pathamoot areas were also vacated. The construction of houses and a school started in the present Pallithura area for those displaced from these areas.