In a model laboratory experiment on infertile arable soil with low biological activity, it was found that the introduction of glyphosate leads to a short-term change in the intensity of the main processes of microbial transformation of nitrogen in the soil. When incubating soil with glyphosate at the maximum recommended dose of 8 l/ha for 22 days, there is an increase in nitrogen-fixing and denitrifying activity by 30–80% and 300% and a decrease in the nitrification process by 20–40%. The effects are of a short-term nature and do not reflect the entire complex of ongoing microbiological processes: no effect of glyphosate was detected on the emission of CO2, which is an integral indicator of biological activity. At the end of incubation in the soil with the introduced glyphosate, there was an increase in the number of bacteria by 40% and a decrease in the number of micromycetes by 70%. In general, under the selected conditions, the introduction of glyphosate led to a marked deterioration in the biological activity of the soil. By the method of multisubstrate testing, it was shown that under the action of the herbicide there is an increase in the value of the coefficient of rank diversity of the consumption spectra of substrates d, accompanied by a decrease in the specific metabolic work W and the integral vitality index G. It was shown for the first time that when glyphosate is introduced into soil with low biological activity and availability of phosphorus and the herbicide is degraded along the sarcosine pathway with a break in the C–P bond, excluding the formation of toxic metabolites, there is a pronounced negative effect of glyphosate on soil microorganisms, which leads to inhibition of wheat plant growth.