After graduation, Ekimov moved to the Vavilov State Optical Institute to conduct research. He began studying  semiconductor-activated glasses, known as Schott glasses, and developing theories to explain their color. When the glasses were heated and then cooled, copper chloride crystals formed, as revealed by X-rays, creating blue colors. Smaller crystals produced bluer glass.
In 1981, Ekimov, along with Alexei A. Onushchenko, reported the discovery of quantum size effects in copper chloride nanocrystals in glass, a phenomenon known now known as quantum dots. During his time at the institute he further investigated these system and developed the theory of quantum confinement with Alexander Efros.
Since 1999, Ekimov has been living and working in the United States as a scientist for Nanocrystals Technology, a company based in New York State.