Biomedical applications of plasma require its efficacy for specific purposes and equally importantly its safety. Herein the safety aspects of cold plasma created with simple atmospheric pressure plasma jet produced with helium gas and electrode discharge are evaluated in skin damage on mouse, at different duration of exposure and gas flow rates. The extent of skin damage and treatments are systematically evaluated using stereomicroscope, labelling with fluorescent dyes, histology, infrared imaging and optical emission spectroscopy. The analyses reveal early and late skin damages as a consequence of plasma treatment, and are attributed to direct and indirect effects of plasma. The results indicate that direct skin damage progresses with longer treatment time and increasing gas flow rates which reflect changes in plasma properties. With increasing flow rates, the temperature on treated skin grows and the RONS formation rises. The direct effects were plasma treatment dependent, whereas the disclosed late—secondary effects were more independent on discharge parameters and related to diffusion of RONS species. Thermal effects and skin heating are related to plasma-coupling properties and are separated from the effects of other RONS. It is demonstrated that cumulative topical treatment with helium plasma jet could lead to skin damage. How these damages can be mitigated is discussed in order to provide guidance, when using atmospheric pressure plasma jets for skin treatments.