Cavitation, which yet has not found a wide application in industrial technologies, is an effective method of hydro-mechanical intensification of chemical-engineering, food, pharmaceutical, biological and other processes. The effectiveness of cavitation process is enabled by cavitation crashing of the solid phase, turbulent diffusion of boundary layer of the fluid by cavitation bubbles, emergence mass transfer aspects, which are characterized by high values of mass transfer coefficients. Processing of biological objects in a cavitation field can be used as an independent process and ensure an inactivation and extinction of microorganisms or as cyanobacteria pre-treatment stage with the aim of increasing the mass transfer surface for the following extraction or biochemical processes. The results of microscopic analysis showed that for certain modes of processing of liquid substances in the cavitation field the decrease of contrast cells is observed as well as damage to the cell membrane, reducing the clarity of contours, cell shape change, aggregation and mechanical damage. Experimental studies have established that in the case of hydrodynamic cavitation to increase the effectiveness of the process of obtaining energy from cyanobacterial biomass, treated in a hydrodynamic cavitation field cyanobacterial biomass, a degree of lipid extraction is increased by 54,3 % and the number of synthesized biogas increases by 28,3 %.