Simple SummarySoil is the basis for providing “fertile ground” for agriculture, including the growth of food and bioenergy crops. The nutrients needed by plants can be provided by chemical fertilizers. However, the heavy usage of fertilizers not only restricts crop production but also destroys the soil environment. Meanwhile, the soil microbiome, an indicator of soil quality that can affect plant growth and yield production, also changes. To solve this problem, a network-structured nanocomposite was prepared for use as a soil conditioner (SC). It was shown that this SC has a good ability to control nutrient loss; advance the agronomic traits of pepper, including growth and yield; improve soil physicochemical properties; and facilitate changes to the composition of microbial communities. With the view that the soil microbiome could develop soil function, we analyzed the correlation between network-structured nanocomposites and soil, microorganisms, and plants. In conclusion, nanonetwork-structured SC is an ideal technology that is effective for the promotion of crop growth and the improvement of the soil microbial community.AbstractFertilizer application can increase yields, but nutrient runoff may cause environmental pollution and affect soil quality. A network-structured nanocomposite used as a soil conditioner is beneficial to crops and soil. However, the relationship between the soil conditioner and soil microbes is unclear. We evaluated the soil conditioner’s impact on nutrient loss, pepper growth, soil improvement, and, especially, microbial community structure. High-throughput sequencing was applied to study the microbial communities. The microbial community structures of the soil conditioner treatment and the CK were significantly different, including in diversity and richness. The predominant bacterial phyla were Pseudomonadota, Actinomycetota, and Bacteroidota. Acidobacteriota and Chloroflexi were found in significantly higher numbers in the soil conditioner treatment. Ascomycota was the dominant fungal phylum. The Mortierellomycota phylum was found in significantly lower numbers in the CK. The bacteria and fungi at the genus level were positively correlated with the available K, available N, and pH, but were negatively correlated with the available P. Our results showed that the loss of nutrients controlled by the soil conditioner increased available N, which improved soil properties. Therefore, the microorganisms in the improved soil were changed. This study provides a correlation between improvements in microorganisms and the network-structured soil conditioner, which can promote plant growth and soil improvement.