Boyd was arrested at least six times but somehow evaded incarceration. By late July 1862, detective Allan Pinkerton had assigned three men to work on her case. She was finally captured by Union officials on July 29, 1862, after her lover gave her up, and they brought her to the Old Capitol Prison in Washington, D.C. the next day. An inquiry was held on August 7, 1862 concerning violations of orders that Boyd be kept in close custody. She was held for a month before being released on August 29, 1862, when she was exchanged at Fort Monroe. She was arrested again in June 1863, but was released after contracting typhoid fever.