Chatterjee studied at the Free Church institution during a tumultuous time in India. The Indian Uprising of 1857 occurred at this time, drawing sharper distinctions between Indian Christians and other religious communities and causing some Indian Christians to reflect more thoroughly on their relationship with Western missionaries. Also, in 1855 a dispute arose within the Free Church mission establishment when a group of its Indian missionaries who were recently ordained applied to join the Mission Council, the main executive arm of the Free Church's mission activities in Bengal. All incoming Scottish missionaries were automatically accepted to the Council but Indian missionaries were not permitted to join. One of the three ordinands who protested this policy was Lal Behari Day with whom Chatterjee became close. The 1855 dispute along with the Uprising of 1857 caused Day to lament, “It is a fact… that the relation subsisting between Missionaries and Native Christians is not of a very satisfactory character.” These events influenced Chatterjee and other classmates such as Kali Charan Banerjee to seek greater equality with Western missionaries.