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Pyrethroids are insecticides most commonly used for insect control to boost agricultural production. The aim of the present research was to determine the effect of permethrin and cypermethrin on cultured and non-cultivated bacteria and fungi and on the activity of soil enzymes, as well as to determine the usefulness of <i>Zea mays</i> in mitigating the adverse effects of the tested pyrethroids on the soil microbiome. The analyses were carried out in the samples of both soil not sown with any plant and soil sown with <i>Zea mays</i>. Permethrin and cypermethrin were found to stimulate the multiplication of cultured organotrophic bacteria (on average by 38.3%) and actinomycetes (on average by 80.2%), and to inhibit fungi growth (on average by 31.7%) and the enzymatic activity of the soil, reducing the soil biochemical fertility index (BA) by 27.7%. They also modified the number of operational taxonomic units (OTUs) of the <i>Actinobacteria</i> and <i>Proteobacteria</i> phyla and the <i>Ascomycota</i> and <i>Basidiomycota</i> phyla. The pressure of permethrin and cypermethrin was tolerated well by the bacteria <i>Sphingomonas</i> (clone 3214512, 1052559, 237613, 1048605) and <i>Bacillus</i> (clone New.ReferenceOTU111, 593219, 578257), and by the fungi <i>Penicillium</i> (SH1533734.08FU, SH1692798.08FU) and <i>Trichocladium</i> (SH1615601.08FU). Both insecticides disturbed the growth and yielding of <i>Zea mays</i>, as a result of which its yield and leaf greenness index decreased. The cultivation of <i>Zea mays</i> had a positive effect on both soil enzymes and soil microorganisms and mitigated the anomalies caused by the tested insecticides in the microbiome and activity of soil enzymes. Permethrin decreased the yield of its aerial parts by 37.9% and its roots by 33.9%, whereas respective decreases caused by cypermethrin reached 16.8% and 4.3%.