<p>Phytochemicals are indispensable to medicine and nutrition, yet their conventional production faces a sustainability crisis due to intensive resource consumption and environmental degradation. This review introduces a holistic “gene-to-final-product” pipeline, a paradigm shift that synergistically integrating upstream biotechnological tools, including metabolic engineering and synthetic biology, with downstream green processing technologies. In contrast to previous studies that have treated these fields as separate disciplines, this work provides a timely and integrative synthesis of their synergy by framing a complete value chain from genetic design to the final product. The review evaluates key strategies for enhancing biosynthetic pathways, designing novel production routes in microbial cell factories, and implementing sustainable extraction methods. The power of this integrated model is demonstrated through compelling synergistic effects; for example, higher phytochemical yields achieved via metabolic engineering can make milder, greener extraction methods economically viable. Practical case studies, including the industrial-scale production of paclitaxel and artemisinin and the valorization of waste streams into polyphenols, validate the feasibility and potential of these integrated systems. By framing these advancements within Green Chemistry principles and the UN Sustainable Development Goals, this review provides actionable insights for a necessary transition toward a circular bioeconomy and sustainable industrial biomanufacturing.</p>