Magnetorheological elastomers are a type of smart hybrid material which combines elastic properties of a soft elastomer matrix with magnetic properties of magnetic micro particles. This composition creates a complex interplay of magnetic and elastic phenomena. The best known is the magnetorheological effect which describes the alteration of the Young's modulus with external magnetic fields. The particle properties and their arrangement in the material play a major role in determining the resulting effects. In this paper X-ray microtomography has been utilized to analyze the particle microstructure. Besides a characterization of the particle microstructure in presence of magnetic fields, here the in-situ observation was combined with an application of mechanical strain. Thus, the situation of the sample during mechanical testing was recreated during tomography to observe the particle microstructure under the exact circumstances of occurring magnetorheological effects. A significant impact of the magnetic field and the strain on the rotation of the particles and their radial distribution was verified.