This work was aimed at experimental investigations of deactivation of different types of microorganisms by using atmospheric pressure low-temperature microwave microplasma source (MmPS). The MmPS was operated at standard microwave frequency of 2.45 GHz. Its main advantages are simple and cheap construction, portability and possibility of penetrating into small cavities. The microplasma deactivation concerned two types of bacteria (Escherichia coli, Bacillus subtilis) and one fungus (Aspergillus niger). The quality as well as quantity tests were performed. The influence of the microorganism type, oxygen concentration, absorbed microwave power, microplasma treatment time and MmPS distance from the treated sample on the microorganism deactivation efficiency was investigated. All experiments were performed for Ar microplasma and Ar/O2 microplasma with up to 3% of O2. Absorbed microwave power was up to 50 W. The Ar flow rate was up to 10 L/min. The sample treatment time was up to 10 s.