The physical and chemical properties of the soil are important factors influencing the yield of crops. One of the agrotechnical factors influencing the biochemical properties of soil is sowing density. It affects the yield components, light, moisture and thermal conditions in the canopy and the pressure of pests. Secondary metabolites, many of which are known to act as a defense mechanism against insects, are of importance in the interaction between the crop and abiotic and biotic factors of the habitat. To the best of our knowledge, the studies conducted so far do not sufficiently reveal the impacts of the wheat species and the sowing density, together with the biochemical properties of the soil, on the accumulation of bioactive ingredients in the crop plants, and the subsequent impacts on the occurrence of phytophagic entomofauna in various management systems. Explaining these processes creates an opportunity for more sustainable development of agriculture. The study aimed to determine the effect of wheat species and sowing density on the biochemical properties of the soil, concentrations of biologically active compounds in the plant and the occurrence of insect pests in organic (OPS) and conventional (CPS) production systems. The research was conducted on spring wheat species (Indian dwarf wheat—Triticum sphaerococcum Percival and Persian wheat—Triticum persicum Vavilov) grown in OPS and CPS at sowing densities 400, 500, 600 (seeds m−2). The following analyzes were performed: (i) soil analysis: the activity of catalases (CAT), dehydrogenases (DEH), peroxidases (PER); (ii) plant analysis: total phenolic compounds (TP), chlorogenic acid (CA), antioxidant capacity (FRAP); (iii) entomological analysis of the number of insects—Oulema spp. adults and larvae. Performing analyzes in such a wide (interdisciplinary) scope will allow for a comprehensive understanding of the soil-plant-insect biological transformation evaluation. Our results showed that an increase in soil enzyme activity caused a decrease in TP contents in the wheat grown the OPS. Despite this, both the content of TP and the anti-oxidative activity of the ferric reducing ability of plasma (FRAP) were higher in these wheats. Bioactive compound contents and FRAP were most favoured by the lowest sowing density. Regardless of the production system, the occurrence of the Oulema spp. adults on T. sphaerococcum was the lowest at a sowing density of 500 seeds m−2. The occurrence of this pest’s larvae was lowest at a sowing density of 400 seeds m−2. Research on bioactive compounds in plants, biochemical properties of soil and the occurrence of pests make it possible to comprehensively assess the impact of the sowing density of ancient wheat in the ecological and conventional production system, which is necessary for the development of environmentally sustainable agriculture.