The method of microwave sterilisation of liquid media is characterised in that, in the cooling stage, the pressure in the process chamber is reduced at a controlled pace, which makes it possible to keep the liquid medium in constant boiling and evaporating without any overflows, until the pressure is equal to the ambient pressure. In the system, the tight pressure chamber (1) is connected to the source of microwave energy (4) with a waveguide (3), where the chamber interior is connected to the compressor (6) via the pressure converter (5), as well as to the regulation discharge valve (7) and safety valve (8). The output of the pressure converter (5) is connected to the input of the control block (9) fitted with a softwared processor and connected to the data input module (10), and the outputs of the control block (9) are connected to the compressor (6) and the regulation discharge valve (7).
