The single cell irradiation using the tandem-type proton/ion accelerator is previewed for microdosimetry purposes in the biological media (yeast cells). Individual cells can also be targeted within a population to obtain the new in vivo data concerning a bystander effect. Usually the strong focusing systems are used for compression of the beam to µm diameter. In this work we assess the possibility to apply a simple mechanical collimator. The detailed modelling with MCNPX v.2.6 and GEANT4 v.9.1 codes shows that the 1.4‐1.8 MeV proton beam energy deposition can be distributed in the 100 µm cell layer with a narrow collimator. An additional focusing system is needed for single cell irradiation. The method for calculation of the microbeam proton doses deposited in separate cells is prepared for the dose rate prediction in the 1.0‐2.5 MeV proton and 3.5‐3.7 MeV He 2+ ion energy range. The experimental proton beam measurements are performed and compared with modelling data.