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Simple Summary The study evaluated the effects of the application of microbial inoculants (N-fixing Klebsiella planticola and Enterobacter spp.), two rates of composite mineral fertilizers, and their combination on microbial biomass carbon, dehydrogenase and proteinase activity in acid Lessivated Cambisol and yield-related properties of maize and wheat grains in a two-year trial. The results indicated that mineral fertilizers are not, in general, negative for soil microbiota when used in the context of sustainable agriculture without monoculture. It was found that the combined application of microbial inoculants and lower doses of mineral nitrogen, phosphorus, and potassium (NPK) fertilizers, increased the yield of maize and wheat compared to the use of only NPK fertilizers in our case study. The highest values of the examined parameters of soil fertility were determined in the period with better precipitation distribution during the vegetation period of the studied year due to the optimal values of soil moisture and air temperature. Concluding, the authors point out the task of science to offer the producer a solution for conducting intensive agricultural production, which must be economically and ecologically safer. Abstract This study evaluated the effects of the application of microbial inoculants (N-fixing Klebsiella planticola and Enterobacter spp.), two rates of composite mineral fertilizers, and their combination on microbial biomass carbon (MBC), dehydrogenase (DHA), and proteinase activity (PTA) in Lessivated Cambisol and yield-related properties of maize and wheat grains in a two-year trial. Unfertilized soil was used as a control variant. MBC was measured using the chloroform fumigation-extraction method, DHA was determined spectrophotometrically by measuring the intensity of the formed red-colored triphenyl formazan, while PTA was determined using a titration method by measuring the degree of gelatine decomposition. In grain samples, P was determined spectrophotometrically, K—by flame emission photometry, N—on an elemental carbon/nitrogen/sulfur (CNS) analyzer, and crude proteins—by calculation of N content. Measuring both crops’ yield was carried out at the end of the vegetation. The results indicated that mineral fertilizers are not, in general, negative for soil microbiota when used in the context of sustainable agriculture without monoculture. There is a significant increase in the values of soil MBC, DHA, and PTA in the variants with combined application of bacterial inoculants and lower rates of mineral fertilizers. The highest values of these parameters were determined in the period with a better distribution of precipitation during the vegetation period of the year. The mentioned combination also resulted in a higher grain yield of maize and wheat comparing to the application of lower rates of the NPK nutrients solely. The combined application of high rates of mineral fertilizers and bacterial inoculants resulted in significantly increased N, P, K, and protein content in the grains of crops, and the same applied to yield. Concluding, studied bacterial inoculants can be used to specify the replacement of nitrogen fertilizers, stimulating the microbial biomass and enzyme activity in the soil, helping to ensure that the supply of nutrients contributing to an optimized yield of crops is maintained.