The agri-food sector generates massive amounts of waste, generating serious environmental and social problems. In the frame of the Circular Economy concept, Biotechnology is envisioned as a reservoir of techniques that can be adapted and applied to transform agricultural waste in new products. In this context, plant-waste extracts, rich in bioactive compounds, are emerging as key players able to improve plant growth and crop productivity to sustainably address food security. To use this recourse, there is the need for safe, cheap, and sustainable technologies to recover these bioactive molecules, while avoiding the use of toxic organic solvents or expensive equipment. One such approach includes the use of beneficial bacteria, like Bacillus subtilis, naturally equipped with enzymes able to target complex plant polymers. The use of bacteria is combined with extraction methods based on isothermal pressurization cycles. The obtained products, rich in polyphenols like rutin, quercetin, ferulic acid, ecc., can be then reincorporated into the agronomic practices as biostimulants (defined as natural bioactive compounds of plant origin, acting as enhancers of plant growth and development), applied as foliar spray, soil irrigation, or as seed treatments or like plant protection products (PPP) towards harmful microorganisms as well. Additionally, such eco-friendly agricultural practices seek to mitigate environmental harm, ensuring long-term food production and economic stability. At a molecular level, the stimulating effects of such treatments on plant growth and stress resilience are mainly related to a substantial boost in the antioxidant defense. Advanced molecular techniques such as transcriptomics, metabolomics, and proteomics can provide deeper insights into the biochemical and molecular responses of plants treated with these bioactive compounds. Therefore, these biotechnological innovations not only aligns with the principles of the Circular Economy but also represent a sustainable strategy to enhance agricultural productivity while minimizing environmental impact.