In the autumn of 1848, Elizabeth returned to Geneva College for her second term after her time at Blockley Almshouse. In the dissecting room, she was surrounded by male classmates who respected her competence. However, Elizabeth's presence outside the classroom was still a source of scandal in Geneva. Her only close friend, George White Field, faced rumors that forced them to limit their interactions. Elizabeth came to appreciate the isolation, as she found it easier to focus on her studies without the distraction of social interactions. She maintained correspondence with her family, particularly Emily, whom she encouraged to join her in the medical field. She also had a visit from her brother, Howard, who planned to move to England with Anna. Elizabeth's sense of responsibility and mission intensified as her family dispersed, leaving her to face the final stretch of her medical education alone.

Elizabeth's determination paid off when she completed her final examinations at the top of her class. The graduation ceremony in January 1849 drew an audience eager to witness a woman receiving a medical diploma. Elizabeth handled the occasion with her characteristic poise and humility, earning applause from the faculty and her peers.