The pharmaceutical, vaccine, and industrial compound industries have tremendous potential for molecular farming, the production of bioactive molecules from genetically modified plants. This chapter provides an introduction to molecular agriculture, including its fundamentals, techniques, applications, and implementation challenges. It discusses plant transformation, gene expression, and the optimization of production systems. Pharmaceuticals, vaccines, and industrial compounds are produced utilizing plant-based platforms. This chapter focuses on the potential for personalized pharmaceuticals and biosimilars derived from botanicals, which provide cost- effective alternatives. New developments in bioreactor systems, genome editing, synthetic biology, and non-traditional plant species are discussed. Regulatory and safety concerns are addressed, including biosafety compliance, Good Manufacturing Practices (GMP), allergenicity, and food safety evaluation. This chapter focuses on future prospects, such as personalized pharmaceuticals, plant-based biosimilars, advanced bioreactor systems, genome editing, synthetic biology integration, multi-stacked traits, and exploration of non-traditional plant species. Collaboration between researchers, industry, regulatory bodies, and the general public is essential for responsible innovation, ethics, and transparent communication. This chapter concludes with an exhaustive summary of molecular agriculture, including its fundamentals, techniques, applications, challenges, and future prospects. It is a valuable resource for researchers, industry professionals, and policymakers interested in using genetically modified plants for cost-effective and sustainable bioactive molecule production.