A doctor in Atlanta diagnosed Flannery with disseminated lupus erythematosus in January 1951, but Flannery’s mother kept it a secret from her. Sally Fitzgerald finally told Flannery that she had lupus not arthritis in June 1952 on a visit to Connecticut. Flannery and her mother moved permanently to Andalusia farm. Regina O’Connor, Flannery’s mother, managed a successful dairy farm on the property. Flannery’s room on the first floor of the main house provided the space she needed to continue her schedule of writing for four hours every morning after attending Mass.

Although Flannery did not plan on moving back to Milledgeville and living with her mother, she made the best of the situation. Flannery got back to her childhood hobby of raising birds. In addition to her old favorites, ducks and chickens, Flannery purchased and raised peacocks. She also started painting in the afternoons after completing her four hours of writing.

Lupus made it difficult for Flannery to lead the independent life she desired, but she did not let it keep her from leading an active life. Whenever her health allowed, Flannery traveled to visit friends, give lectures, and even make TV appearances. Friends and family frequently visited Andalusia and when she could not visit with people in person, Flannery corresponded with them regularly.

In June 1955, Flannery published A Good Man is Hard to Find, a collection of short stories. Many of the short stories were written or rewritten while Flannery lived at Andalusia. The stories included characters inspired by people Flannery came in contact with on the dairy farm or in the surrounding community. In February 1960, Flannery published her second and last novel, The Violent Bear It Away. In February 1964, Flannery had surgery to remove a fibroid tumor. The tumor was successfully removed, but surgery reactivated her lupus and caused kidney infections. Flannery continued to work on her last collection of short stories until July when she simply ran out of energy from poor health. On August 2, 1964 Flannery died of kidney failure at the Baldwin County Hospital in Milledgeville. Her last collection of short stories, Everything That Rises Must Converge, was published after her death in 1965. Flannery O’Connor is buried at Memorial Hill Cemetery in Milledgeville.