Bendur was once a part of the Cathedral and Milagres churches.  Bishop Paul Perini sj constituted Bendur parish on August 23, 1914.   The site and land  to build the church was bought in 1918 from  the nuns of the Apostolic Carmel. A thatched shed was erected by Fr R.F.C. Mascarenhas, the first parish priest (1914-1931) and the founder of the Bethany Congregation.  The foundation stone was for the new church was laid on January 7, 1919.  Rev. Bishop Valerian J. D’Souza blessed the church on January 3, 1930.  Fr F.S. D’Souza (1933-1936) built the presbytery.  Fr Charles B. Lobo (1936-1945) built the façade and the portico.  Fr Albert B. Pinto (1962-1971) secured 3 large bells from West Germany,  built the belfry and installed the bells. The Altar of St Francis Xavier was built during the time of Fr Francis D’Souza.

The eighth parish priest of Bendur, Fr Basil Peres Salvadore (1952), after serving 3 months as the Vicar,  became the Bishop of Mangalore.  The small church hall was built during the time of Fr Albert Pinto.  The sound system was installed by Fr Nicolas Pereira.  Bishop Victor Rosario Fernandes of Mangalore, Bishop Jacob Mendonca of Thiruchirapalli, Bishop Basil Salvadore Peres of Mangalore, Bishop Paul Patrick D’Souza of Varanasi, literary figures like Messrs V.J.P. Saldanha and Louis Mascarenhas, political figures like Mr Blasius M. D’Souza and Ms Judith Mascarenhas are from this parish.  

In 1919 a school in the church compound was started.  St Joseph’s school at Kankanady was handed over to the Bethany Sisters. Padua High School was established in 1944.  This school was known as Bishop Victor Fernandes School and was not under the parish.  In the year 2000 it was handed over to Bendur parish by the Catholic Board of Education, Mangalore.  In 1986, the School of St Margaret Mary was merged with St Sebastian School since the number of students was too small for two schools in the same locality.