The effect of commercial humic product Lignohumate ® on the biological activity of Latosol under long-term agricultural use with application of pesticides at the Bali Island (Indonesia) was evaluated in model experiments. It was shown that the application of lignohumate in a concentration gradient 0.025–2.5 mg/g resulted in increase in soil microbial community respiration rate by 10–30%, proportionally to the rate applied. As the application rate of Lignohumate increased, a significant threefold increase of nitrogen fixation intensity caused by the activation of bacteria of the Oxalobacteriaceae family was observed. In general, the bacterial community of Latosol consisted of more than 85% of the representatives of four phyla: Proteobacteria, Firmicutes, Chloroflexi, and Acidobacteria. Lignohumate at application rates higher than 0.025 mg/g promoted an increase of methane formation, whereas gaseous nitrogen losses due to denitrification reduced. An important practical conclusion on the reduction of a toxic effect of pesticides in the presence of lignohumate and its positive effect on soil biological activity and nitrogen balance in the Latosol under intensive agricultural use was made.