The rooms at the back of the church were meant to be the residence of the priests in charge. But when Solaroli donated his palace to the Missions, the Fathers shifted there. The place they vacated was ideal for a convent school. In 1848, Mother Mary St. Gonzaga of the Congregation of Jesus and Mary started this convent, which was then a boarding school for European girls. Several additions were necessary to provide for dormitories, class-rooms and a refectory. But in 1857 the school was considered unsafe for European girls and was closed. But it opened the following year as an orphanage for Indian girls. In 1902, Dr. Charles Gentili, Archbishop of Agra, handed over the management of the school to the Clarist Franciscan nuns from Bertinoro (Italy). But after 5 years the nuns of Jesus and Mary were recalled by the same Archbishop to take over the school again.

In 1922 the nuns were asked to shift their school to Anthon Kothi, the former residence of Anthony Regelini, the architect of the church and palace. The nuns enlarged and improved the building. The reason for this transfer was that the Archbishop required the school building and its proximity to the church for a Capuchin Novitiate. The convent had to undergo extensive repairs to meet the requirements of a Novitiate. The convent had to undergo extensive repairs to meet the requirements of a Novitiate. But in 1930 the Novitiate was transferred to Mangalore, and so the nuns were back again in 1931.

n 1936, the school was recognised as a Middle school. In 1951 it was raised to a Junior High School. Then in June 1961 it reached High School status. In 1965 it was recognised as an Intermediate College and in 1983 it became a B. A. College. St. Joseph's Convent has the privilege of being one of the oldest institutions in North India, and the Congregation of Jesus and Mary the distinction of being the first congregation of nuns in the North.