Strong gravitational lensing leads to an occurrence of multiple images, with different magnifications, of a lensed source. Those magnifications can in turn be modified by microlensing on smaller mass scales within the lens. Recently, measurements of the changes in the magnification ratio of the individual images have been proposed as a powerful tool for estimation of the size and velocity of the emission region in the lensed source. The changes of the magnification ratios in blazars PKS1830-211 and QSO B0218+357, if interpreted as caused by a microlensing on individual stars, put strong constraints on those two variables. These constraints are difficult to accommodate with the current models of gamma-ray emission in blazars. In this paper we study if similar changes in the magnification ratio can be caused by microlensing on intermediate size structures in the lensing galaxy. We investigate in details three classes of possible lenses: globular clusters (GCs), open clusters (OCs) and giant molecular clouds (GMCs). We apply this scenario to the case of QSO B0218+357. Our numerical simulations show that changes in magnifications with similar time-scales can be obtained for relativistically moving emission regions with sizes up to 0.01 pc in the case of microlensing on the cores of GCs or clumps in GMCs. From the density of such structures in spiral galaxies we estimate however that lensing in GMCs would be more common.