Matkin left the Navy after the voyage of HMS Challenger. He took employment with the civil service, and moved to London with his wife, Mary "Pollie" Swift, whom he'd married in 1880. They had six sons. He retired at 41, and not much is known about his later life, particularly how he came by the means to support his large family after his young retirement. He died in 1927, as the result of an accident, variously described as a fall, a motor vehicle accident, and a pedestrian vs. motorcycle accident.

Joseph and Mary Matkin and their sons. 1907.