Owing to their wide range of applications in the control of ticks and insects in horticulture, forestry, agriculture and food production, pyrethroids pose a significant threat to the environment, including a risk to human health. Hence, it is extremely important to gain a sound understanding of the response of plants and changes in the soil microbiome induced by permethrin. The purpose of this study has been to show the diversity of microorganisms, activity of soil enzymes and growth ofZea maysfollowing the application of permethrin. This article presents the results of the identification of microorganisms with the NGS sequencing method, and of isolated colonies of microorganisms on selective microbiological substrates. Furthermore, the activity of several soil enzymes, such as dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal),β-glucosidase (Glu) and arylsulfatase (Aryl), as well as the growth ofZea maysand its greenness indicators (SPAD), after 60 days of growth following the application of permethrin, were presented. The research results indicate that permethrin does not have a negative effect on the growth of plants. The metagenomic studies showed that the application of permethrin increases the abundance ofProteobacteria, but decreases the counts ofActinobacteriaandAscomycota. The application of permethrin raised to the highest degree the abundance of bacteria of the generaCellulomonas,Kaistobacter,Pseudomonas,Rhodanobacterand fungi of the generaPenicillium,Humicola,Iodophanus,Meyerozyma. It has been determined that permethrin stimulates the multiplication of organotrophic bacteria and actinomycetes, decreases the counts of fungi and depresses the activity of all soil enzymes in unseeded soil.Zea maysis able to mitigate the effect of permethrin and can therefore be used as an effective phytoremediation plant.