After the end of the war, Stephenson returned to Cambridge to carry out research and teach in the department of biochemistry. Under the leadership of Frederick Gowland Hopkins, a group of scientists became the centre of modern biochemical studies. Here Stephenson began research on bacteria and their metabolism. The department had an unusually high proportion of women amongst its researchers (15 per cent), but it was still very rare for a woman to be offered a University appointment. Stephenson was financed by her Beit Fellowship and later by the Medical Research Council. She was finally appointed a University lecturer in biochemistry in 1943. Meanwhile, she became an associate and later a fellow of her old College, Newnham. In 1936 the University awarded her an ScD degree for her research.