In 1942 he obtained his Abitur, but because of the Second World War he was only able to start studying physics at Leiden University in 1945.

In 1951, after intermittent military service, he received his diploma in meteorology and in 1954 he received his doctorate in low temperature physics from Cornelis Jacobus Gorter and Krijn Wybren Taconis from the Kamerlingh-Onnes Laboratory at Leiden University.

Beenakker remained in Leiden after graduation, where he became a lecturer in 1959 and a full professor of experimental physics in 1963.

The Senftleben-Beenakker effects are named after him and the German physicist Hermann Senftleben, which describe the influence of electric and magnetic fields on the transport properties (thermal conductivity, viscosity) of molecular gases.

From earlier experiments by Senftleben it was believed that this only affected paramagnetic molecules such as nitric oxide and oxygen, but Beenakker and his colleague Hein Knaap showed that diamagnetic gases such as nitrogen and methane are also affected by external fields (but they should have a non-spherical shape have), since the precession rate between two collisions of the molecules is changed by them.