Soil phytopathogenic nematodes cause great damage to agricultural plants. Different methods have been used to control them. However, this issue still requires a more effective solution. Caenorhabditis elegans (CGC Strain wild type N2) was applied as a model with E. coli OP50 used as a feeding substrate for nematodes. Our approach was based on the thermodynamically substantiated creation of growth conditions unfavorable for nematodes to suppress them irreversibly. Nematodes control effect was also enhanced via the application of the strain Pleurotus ostreatus Po4. It is based on the study of the impact of key parameters such as pH, redox potential (Eh, mV), and O2 presence as well as P. ostreatus Po4 and bacteria (Escherichia coli OP50 and a native microbial community of compost of plant residues) on nematodes. As a result, the patterns of C. elegans N2 inhibition were studied. The creation of anaerobic conditions via the application of P. ostreatus Po4 and bacteria provided the irreversible suppression of nematodes. This research contributes to the development of the foundations to preserve agricultural plants, and increase crop yield as well as the approach for environmentally friendly control of phytopathogens.