The IEM was established in 1976. Initially, the Institute was formed by several researchers working on the fields of Particle Physics, Molecular Physics, Quantum Chemistry, and Crystalline Polymers, with only five scientists on staff. Nowadays the Institute's core mission is to enhance knowledge on the structure of matter in a wide range of physical scales, from the building blocks of matter and space-time, to nuclei, atoms, molecules, and macromolecules, including condensed matter and mesoscopic systems.

Research activities are organized around groups, both experimental and theoretical, covering fields of Gravitational, Nuclear, Statistical, Atomic, Molecular, and Macromolecular Physics. Part of this research is based on large national and international facilities, such is the case for the groups of Experimental Nuclear Physics, Statistical Physics, and Macromolecular Physics.

Currently, the IEM comprises about 45 staff scientists. IEM participates in over 60 research projects, yielding an average of 165 publications per year in prestigious scientific journals. Staff scientists, along with support staff, students and hired personnel add up to about 135 people.

Since 1994 the IEM belongs to the "Miguel Antonio Catalán" Physics Center (CFMAC) .

Its facilities and laboratories are located in four buildings at the main CSIC campus on Serrano St. in Madrid , which also house the facilities of the Institute of Optics and the Institute of Fundamental Physics .