Mohnhaupt was born in Rheinberg, North Rhine-Westphalia, the daughter of an employee in a publishing house.
After her parents' divorce in 1960 she stayed with her mother. She took her abitur in 1967 in Bruchsal, and later that year enrolled with the philosophy department at the University of Munich. She was married to Rolf Heissler from 1968–1970. While in Munich, she joined the local commune scene, where she met core figures of the 1960s student movement such as Rainer Langhans, Fritz Teufel and Uschi Obermaier. In 1969, she participated in a demonstration in the USA cultural centre in Munich (Amerikahaus) to protest against the Vietnam War. She was reportedly influenced by Carlos Marighella's Manual of the Urban Guerilla.