<p>India, as the second-largest global producer of fruits and vegetables, faces a substantial challenge due to a high level of post-harvest waste estimated at 30% annually for fruit and totalling 163 million tonnes of vegetable production, equivalent to 81.5 million tonnes. This waste, primarily due to inefficiencies in transportation, storage, and processing by-products, poses significant environmental and health risks. Conventional methods, such as food processing waste as fertilizer or animal feed, must sufficiently address the environmental impacts. This study explores the potential of plant growth-promoting rhizobacteria (PGPR), specifically <i>Bacillus subtilis</i>, as an innovative solution for waste management and agricultural sustainability. The research involves isolating <i>Bacillus subtilis</i> from pomegranate peel and confirming its viability through DNA extraction, 16S RNA sequencing, and biochemical testing. A pot experiment was conducted with wheat grains treated with <i>Bacillus subtilis</i>, pomegranate peel, and a control group. A qualitative phytochemical analysis was also performed to examine chlorophyll, phenol, and antioxidant content in <i>Bacillus subtilis</i>-treated wheatgrass microgreens. The study found that <i>Bacillus subtilis</i> treatment resulted in increased plant height and total yield in wheat compared to both the pomegranate peel and control groups. Furthermore, wheatgrass microgreens treated with <i>Bacillus subtilis</i> exhibited higher levels of phenols and antioxidants, indicating enhanced nutritional value. This study highlights the potential of <i>Bacillus subtilis</i> as a biofertilizer to address agricultural waste management challenges while boosting the nutritional content of produce. Integrating <i>Bacillus subtilis</i> as a biobased solution offers a pathway toward a more eco-friendly and resilient agricultural system, supporting sustainable agriculture and improved waste management practices.</p>