Kennedy returned to Benares in 1854 to resume missionary work. Her husband became the superintendent of the London Missionary Society’s school in Benares, and Margaret spent time teaching children at the school. Kennedy devoted much of her time to working people, especially women and children from all social and ethnic backgrounds, spending as much time as possible with young women. Kennedy and her children left Benares in 1857 due to the Indian Mutiny and did not return until 1859. Upon returning, Kennedy continued her work, preaching and working with her day school, as she focused her work especially among native women. She is considered one of the first zenana missionaries in India.