Natural products are a vital source of therapeutic agents due to their diverse chemical structures and wide range of biological activities. With the advancement of computational technologies, natural product databases have become essential tools in drug discovery, offering organized access to chemical structures, biological properties, and biosynthetic information. These databases support various stages of drug development, from target identification to lead optimization. This review outlines the essential features of Natural Products Databases and introduces the framework for the first Libyan Natural Products Database, a project designed to harness Libya’s unique biodiversity. This foundational work involves a detailed review of existing natural product databases to identify their core components, data architectures, and user interface designs. While acknowledging challenges such as data standardization, limited resources, and long-term sustainability, the creation of the Libyan Natural Products Database is expected to enhance local scientific capacity and contribute meaningfully to the global drug discovery landscape. This positions the Libyan Natural Products Database to play a foundational role in advancing pharmaceutical research and drug discovery.