Green synthesis of nanomaterials represents a sustainable, safe, and cost-effective alternative to conventional chemical and physical approaches for nanoparticle fabrication. In contrast to many existing review articles that focus exclusively on a single category of biological resources, this work presents the first truly integrated and comprehensive review that systematically examines the full spectrum of biological sources—encompassing microorganisms (bacteria, fungi, algae, and yeasts), plant extracts, purified biomolecules (including proteins, amino acids, carbohydrates, and lipids), and animal-derived materials (such as chitosan, honey, silk, and egg components)—within a unified analytical framework. The review thoroughly elucidates intracellular and extracellular synthesis mechanisms, the critical roles of key functional groups (e.g., hydroxyl, carboxyl, amine, and thiol), and the process parameters governing synthesis efficiency—including pH, temperature, extract concentration, type of metal salt, and reaction time. Furthermore, it critically evaluates structural and functional differences among various green synthesis strategies and addresses the major challenges hindering industrial-scale commercialization. These include nanoparticle size and morphology heterogeneity, low conversion yields of metal ions, seasonal and geographical dependencies on plant-based resources, and excessive energy consumption in certain thermal protocols. By aligning closely with the principles of green chemistry and offering a strategic, holistic roadmap, this review lays the groundwork for the development of next-generation, environmentally compatible nanobiotechnologies with broad applicability across diverse fields—without being restricted to any single application domain such as agriculture.