Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the relationships of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types on the food web active communities in the rhizosphere and bulk soil compartments. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial–microfaunal ecological relationships, with inter- and intra- connections among primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that the addition of organic fertilization selects bacterial orders with important inter-kingdom ecological interactions for survival, predation and cooperation. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.