His thesis was entitled Topics in intuitionism and topos theory and was written under the supervision of Anne Sjerp Troelstra.

[7] Moerdijk received the 2011 Descartes-Huygens prize for his contribution to French–Dutch scientific collaborations from the Académie des Sciences in Paris.

[1][10][11] Moerdijk's research interests lie in the fields of category theory, algebraic and differential topology, and their applications to mathematical logic.

[12][13] In 1992 he wrote, together with Saunders Mac Lane, a book on topos theory that became the standard reference on the subject: Sheaves in geometry and logic.

[15] Moerdijk's research has also covered topics in differential geometry; in particular, he wrote in 2003 an influential monograph on foliations and Lie groupoids.