Background and Aims <p>Given the ongoing environmental degradation and increasing agricultural intensification, the use of fertilizers enriched with beneficial microorganisms (biofertilizers) is an environmentally friendly alternative to chemical fertilizers. The aim of the study was to assess microbial activity and diversity in degraded soils following the application of selected fungal (<i>Aspergillus niger</i> and <i>Paecilomyces lilacinus</i>) and bacterial strains (<i>Bacillus</i> sp., <i>B. amyloliquefaciens,</i> and <i>Paenibacillus polymyxa</i>), both with and without NPK fertilization, and to evaluate their effect on maize yield.</p> Methods <p>Two-years field experiment was conducted on Brunic Arenosol and Abruptic Luvisol under maize from which samples were collected. The laboratory experiment included the determination of maize yield, soil physico-chemical parameters, and microbial activity and diversity.</p> Results <p>The obtained results revealed an increase in crop yield (<i>p</i> &lt; 0.05) and different responses of soil parameters to additives used. PERMANOVA confirmed that term of sampling and soil type significantly affected microbial parameters (<i>p</i> &lt; 0.001), and their effect combined with fertilizers was also significant (<i>p</i> &lt; 0.001). Most of the applied additives were more stressful to microorganisms inhabiting the nutrient-deficient sandy Arenosol than to those in the more fertile silty Luvisol. Although the additives used had no significant effect on some of the measured microbiological parameters, the addition of bacteria had a more pronounced effect (<i>p</i> &lt; 0.05) than the addition of fungi.</p> Conclusion <p>In the sustainable management of intensively cultivated agricultural soils, current research underscores the critical importance of baseline soil nutrient levels in guiding the formulation and optimization of (bio)fertilization strategies.</p>