He is well known for his work on computer security, on programming languages, and machine learning. In security, Abadi developed (with Michael Burrows and Roger Needham) the Burrows–Abadi–Needham logic for analyzing authentication protocols, and with Needham received the IEEE S&P Test of Time award for his work Prudent engineering practice for cryptographic protocols.

In programming language research, he published a book (with Luca Cardelli) A Theory of Objects, laying out formal calculi for the semantics of object-oriented programming languages. Additionally, In 1993, he published the programming language Baby Modula-3, a safe subset or sublanguage of Modula-3, based on functional programming and set theory ideals.