Encouraging farming practices employing fruit waste as a biofertilizer is the key to promoting sustainable agriculture. This study highlights the potential of using fruit waste, specifically pomegranate peels, as a biofertilizer to promote sustainable agriculture. The main objective was to evaluate the effect of Bacillus subtilis (probiotics) derived from fruit peels on fenugreek microgreens’ growth and nutritional properties. The experiment was conducted in Coimbatore, India, where Bacillus subtilis was isolated from fruit peels like pomegranate, orange, and sweet lime. DNA extraction and PCR amplification were used to identify the bacterial strain. The study found that Bacillus subtilis from pomegranate peels (Bs. PP) was most effective in improving plant growth and nutrition. Fenugreek seeds were sown, and soil was treated with the Bacillus subtilis KR strain (Bs. PP) from pomegranate peels, pomegranate peels alone, and a control was used for comparison. The results showed that plants treated with Bs. PP had the highest total phenolic, antioxidant, and chlorophyll content. The total phenolic content increased by 2.46%, and the antioxidant content was four times higher than in soil treated with pomegranate peels alone. The findings suggest that incorporating Bacillus subtilis from pomegranate peel waste could improve crop production and nutritional quality, supporting more sustainable agricultural practices and environmental health.