Manna returned to Israel in 1972 as a professor of applied mathematics at the Weizmann Institute of Science. He became a full professor at Stanford in 1978. He remained affiliated with the Weizmann Institute of Science until 1995. He continued to work as a Stanford professor until retirement in 2010.
He authored nine books. The Mathematical Theory of Computation (McGraw Hill, 1974; reprinted Dover, 2003) is one of the first texts to provide extensive coverage of the mathematical concepts behind computer programming.
With Amir Pnueli, he co-authored an unfinished trilogy of textbooks on temporal logic and verification of reactive systems: The Temporal Logic of Reactive and Concurrent Systems: Specification (Springer-Verlag, 1991), The Temporal Logic of Reactive and Concurrent Systems: Safety (Springer-Verlag, 1995) and The Temporal Logic of Reactive and Concurrent Systems: Progress (unpublished; first three chapters posted at http://theory.stanford.edu/~zm/tvors3.html).
In 1994 he was inducted as a Fellow of the Association for Computing Machinery. In 2016, he shared the Herbrand Award with Richard Waldinger for his ″pioneering research and pedagogical contributions (with Richard Waldinger) to automated reasoning, program synthesis, planning, and formal methods″.. He received Bauer Prize from the Technical University of Munich as well as an honorary doctorate from the École Normale Supérieure de Cachan.