The lectures and hostel swiftly became Newnham College, and Anne Jemima Clough its first Principal. The new college took a different approach to women’s education to Girton College, recognising that women had been denied the educational opportunities available to their brothers. A later biographer described her as follows, “she had inexhaustible good humour, plenty of common sense and fun, and an enviable ability to admit when she was wrong. These qualities made her students cherish her and enabled her to work well and creatively with her colleagues.” Though she had little experience of administration, she oversaw the building of the new college and negotiations over leasing the land. Her personality, commitment and drive made her “a recognised leader in the education of women”. She was cared for at the end of her life by her niece Blanche Athena Clough and her friend Edith Sharpley who was the classics lecturer. They were both present when she died at Cambridge on 27 February 1892. Two portraits of Clough are at Newnham College, one by Sir William Blake Richmond, the other by James Jebusa Shannon. Her grave is in Grantchester churchyard, near Cambridge. Her legacy is marked in Clough Hall and the Clough memorial gates at Newnham College, a stained glass window at Liverpool Cathedral, the Hope Street sculpture "A Case History" in Liverpool. Her birth place in Liverpool is marked with a plaque, commemorating both Anne Jemima and her brother Arthur Hugh. Edge Hill University has a hall of residence called Clough in honour of her contribution to higher education and the history of education in Lancashire.