Minute examination of local lattice structures in matter affected by impurity doping is of special importance for the development of functional materials. In order to obtain microscopic information on spinel ferrites, in the present work, we introduced nonmagnetic In3+ ions in Fe3O4 and probed their site selectivity and the doping effect on the local lattice structures and bulk magnetism by means of 57Fe Mössbauer spectroscopy and positron annihilation spectroscopies. The Mössbauer parameters of the area intensity and isomer shift (IS) show that In3+ ions predominantly reside in the tetrahedral A site, especially at low doping level. With increasing concentration of In ions, however, they gradually occupy the octahedral B site replacing Fe3+ ions. Along with the site information, the IS values confirmed that the introduced In ions squeeze the B-site Fe ions at their nearest neighbors. Supporting results were obtained from positron annihilation lifetime spectroscopy; positron lifetimes become shorter with increasing In concentration, signifying that the oxygen ions are pressed by the introduced In ions resulting in lowering the volume of the adjacent lattice vacancies. The results of Doppler broadening spectroscopy also support the squeezing effect; the positrons in the vacancies adjacent to In ions are more likely to annihilate with the inner shell electrons of the surrounding oxygen ions as a result of a reduction in the vacancy volume.