The aim of this study was to determine the impact of intercropping of permanent plantation and agricultural crops on biodiversity, community structure and indices of soil disturbance and ecological diversity, as well as on fertility parameters and yield. For the purpose, from 2017 to 2019 experiments were conducted at two sites (Ivankovo and Đakovo) with three different ecosystems: the intercropping ecosystem of agricultural crops and walnut (K + O), the ecosystem of walnut (O) and the ecosystem of agricultural crops (K). The K+O ecosystem showed a positive influence on the diversity index H', the total and average diversity of genera, especially on the diversity of beneficial omnivores, indicating the stability of the ecosystem. Bacterivores were significantly more numerous in ecosystem K, and fungivores in ecosystem O. Unlike these ecosystems, ecosystem K+O indicates decomposition of organic matter by both bacterial and fungal pathways. The values of MI and MI 2- 5 indicate the greatest disturbances in ecosystem K. CI values in ecosystem O indicate a higher proportion of fungi and fungivores involved in organic matter decomposition. BI and EI values in all ecosystems indicate that the soil is disturbed, but the soil food web is not impoverished. SI values indicate a developed soil food web, a good share of higher trophic groups and resistance to pests in ecosystems K+O and O. Metabolic footprints of nematodes, high activity of bacteria and fungi, higher amounts of organic matter and soil moisture also indicate a positive influence of ecosystem K+O, when compared to ecosystem K. Wheat yields did not differ, while buckwheat yield was lower in ecosystem K+O. In addition, a regression model was created to estimate the number of nematode genera based on the analysis of chemical, physical and microbiological properties of the soil with an accuracy of 87.53% (Đakovo) and 86.68% (Ivankovo).