The production of biohydrogen through dark fermentation represents an important pathway for recovering renewable, carbon-neutral energy from organic waste. However, challenges such as low yield and process instability still limit its scalability. This review provides a detailed overview of the physicochemical and operational factors pH, temperature, inoculum characteristics, organic loading, and reactor configuration that affect microbial performance and hydrogenase activity. In addition to summarizing these fundamental processes, the review introduces a new perspective by incorporating innovations in green materials. Special attention is given to hydroxyapatite (HAP), a sustainable bio-additive derived from waste that enhances cell immobilization, pH buffering, and metabolic stability through the controlled release of Ca2⁺ and PO₄3⁻ ions. A comparative analysis of different synthesis methods for physical, chemical, biological, and waste-based HAP highlights their versatility and potential in promoting a circular economy. By integrating process optimization principles with multifunctional HAP strategies, this review establishes a conceptual link between bioprocess engineering and materials science, offering a framework for developing more efficient, resilient, and environmentally friendly biohydrogen production systems.