This study aimed to explore the effect of sustained application of plant-based compost on soil biological properties in a field where varying quantities of compost have been consistently applied since the inception of cultivation. The field is envisaged as an educational facility for elementary and junior high school students. Disparities in soil biological properties were examined across plots where different quantities of plant-based manure were consistently applied over a decade. Furthermore, the correlation among soil nutrients, carbon and nitrogen contents, and yield and quality of sweet potatoes cultivated under identical conditions in the same plots was established. The results revealed that excessive applications of fertilizer led to a decrease in the number and species of soil organisms and a tendency for an increase in the population of each species. The experimental plots with minimal continuous applications of compost exhibited higher biodiversity. Additionally, this plot produced sweet potatoes of superior quality. In plots where plant-based manure was consistently applied, a fertilizer application rate below the standard value proved suitable for sweet potato cultivation in the tenth year. Therefore, in plots with continuous applications of plant-based compost, a low amount of fertilizer could sustain soil organism diversity and enhance sweet potato quality.