Baerends is known for his development and application of electronic structure calculations, which over time led to the development of the Amsterdam Density Functional. He worked extensively on density functional theory.
Baerends became a member of the Royal Netherlands Academy of Arts and Sciences in 2004. In 2010 he was awarded the Schrödinger Medal by the World Association of Theoretical and Computational Chemists, being noted for: "For his pioneering contributions to the development of computational density functional methods and his fundamental contributions to density functional theory and density matrix theory." Baerends is a member of the International Academy of Quantum Molecular Science.