Conversion of food wastes into bio-organic fertilizers is a rational solution that both reduces the burden on the environment and creates positive impacts on increasing agricultural productivity and securing world food security. Bio-organic fertilizers are mixtures of organic matter decomposition and living microorganisms. There are still unknown points about how these microorganisms carry out beneficial activities to the development of plants and how they interact with other microbes in a competitive environment in soils. This study examines the effects of two types of bio-organic fertilizers converted from either fruit peels or leafy vegetable wastes on the early development of bok-choy (Brassica rapa) and the microbial community in soil. Results indicated that both fertilizers positively impact the germination of bok-choy by increasing the sprouting rates while maintaining the stem development of the plants compatible with plants in the control case with unfertilized soil. The fresh root mass of plants grown in unfertilized soil was statistically higher than that of plants grown in fertilized soils, which correlated with a greater mean root length in this soil condition, although not significantly. A microbial count test pointed out shifts in the microbial populations that grow on Czapek agar (CZA) and De Man, Rogosa, and Sharpe (MRS) agar media. An increase in the lactobacilli population of the soil supplemented with bio-organic fertilizer from fruit peels suggested a connection to the significant increase in soil microbial respiration observed in this environmental condition.