While at Strasbourg in 1981, Markovitsi joined the CNRS. Then she relocated to the Paris area, where she worked from 1985 until 2021 in the CEA Paris-Saclay, in joint research Laboratories of the CNRS and the French Alternative Energies and Atomic Energy Commission. From 2001 to 2014, she was the director of the Francis Perrin Laboratory ().  After being appointed Emeritus Research Director, she moved to the Institut de Chimie Physique - Université Paris-Saclay.
Markovitsi served as president of the European Photochemistry Association from 2007 to 2010, and since 2014 she is the president of the [http://www.asianphotochem.com/doc/20230816_IFPwebpage.pdf International Foundation for Photochemistry].