Crop yield decrease is the main concern when a pathogen or plague is identified in an agriculture field. Thus, part of this issue can be attributed to plant-parasitic nematodes (PPNs), such as Meloidogyne species, due to, most of the time, the hard diagnosis, and non-specific symptoms. Its management is mainly based on chemical pesticides, followed by a few potential biological control agents, and the management system. Therefore, this study aimed to evaluate the effects of biological agents in Meloidogyne incognita control in different soil systems. For that, two biological products were chosen, Trichoderma asperellum BV10 and Bacillus amyloliquefaciens BV03, and soils were sampled from three different managements systems: (i) soybean no-tilled system at Goiás state, Brazil; (ii) forest soil at Goiás state, Brazil, and (iii) soybean conventional managed system at Mato Grosso do Sul state, Brazil. Biocontrol and growth promotion effects, volatile organic compounds (VOCs) and soil respiration were determined in vegetation house and laboratory, respectively. As a result, both BV10 and BV03 had significant nematode control activity, comparing to control treatment, in all the three soils systems. Plus, the number of immobile nematodes by potential VOCs had significant increase when BV03 was applied, while the application of BV10 agent raised the soil respiration rate. In conclusion, both biocontrol agents presented great efficiency in control M. incognita, with better performance of BV03. Lastly, more studies must be done to elucidate how the resident soil microbiome can influence on biocontrol agent establishment and performance, as well as the consequence of the application of biological products on soil microbiome network.