Shortly after his discovery, Zeeman was offered a position as lecturer in Amsterdam, where he started to work in autumn of 1896. In 1900, this was followed by his promotion to professor of physics at the University of Amsterdam. In 1902, together with his former mentor Lorentz, he received the Nobel Prize for Physics for the discovery of the Zeeman effect. Five years later, in 1908, he succeeded Van der Waals as full professor and Director of the Physics Institute in Amsterdam.
In 1918 he published "Some experiments on gravitation: The ratio of mass to weight for crystals and radioactive substances" in the Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, experimentally confirming the equivalence principle with regard to gravitational and inertial mass.
A new laboratory built in Amsterdam in 1923 was renamed the Zeeman Laboratory in 1940. This new facility allowed Zeeman to pursue refined investigation of the Zeeman effect. For the remainder of his career he remained interested in research in magneto-optic effects. He also investigated the propagation of light in moving media. This subject became the focus of a renewed interest because of special relativity, and enjoyed a keen interest from Lorentz and Albert Einstein. Later in his career he became interested in mass spectrometry.