In 1996, she returned to athletics. Instead of only running the 800 m, Masterkova also decided to compete in the 1500 metres, a distance she had not competed in four years. At the Russian Championships, she won both distances in top times. However, she was not considered as a real favourite for the 800 m Olympic gold; Maria de Lurdes Mutola and Ana Fidelia Quirot were expected to fight for the title in Atlanta. Masterkova took the lead from the start, and led the entire race to become Olympic champion. After this surprise, Masterkova caused a major upset by also winning the 1500 m in a similar fashion, thereby equaling Tatyana Kazankina's performance at the 1976 Olympics (Kelly Holmes would repeat the performance in 2004). She completed her season by also setting two new world records at the 1000 metre and mile distances.
Masterkova was not able to repeat her feat at the World Championships the next year, as an achilles tendon injury caused her to drop out in the heats of the 1500 metres. Her 1998 season was great again, crowned by a win in the 1500 m at the European Championships. At the 1999 World championships, Masterkova again contested both middle distance events. She was beaten in the 800 m by Ludmila Formanova and placed third but comprehensively won the 1500 metres title. This would be her last major success. Although Masterkova participated in the Sydney Olympics, she abandoned her 1500 metres heat. She announced her retirement at Znamensky Indoor stadium on January 7, 2003.