Ge/Si quantum dot (QD) structures doped with Mn have been tested by the EPR method to find the optimal conditions for formation of the diluted magnetic semiconductor (DMS) phase inside QDs. The effect of Mn doping has been studied for two series of samples: series A with QDs grown at 450°C and varied Mn concentration and series B with QDs grown at different temperature with Mn concentration x = 0.02. Several effects of modification of the EPR spectra due to Mn presence in the samples have been obtained. These effects are related to (i) strain reduction due to Ge—Si intermixing, (ii) QD enlargement and change in QD shape, (iii) presence of an additional magnetic field produced by Mn atoms incorporated in QDs. The data obtained allow us to understand the reasons for irreproducibility of the results available in the literature on the creation of magnetic Ge 1 − x Mn x quantum dots.