Bio-based fertilisers (BBFs) derived from waste streams represent a transformative approach to sustainable agriculture, addressing the dual challenges of waste management and food security. This comprehensive review examines recent advances in BBF production technologies, nutrient recovery mechanisms, soil health impacts, and the benefits of a circular economy. This review, based on an analysis of peer-reviewed studies, demonstrates that BBFs consistently improve the physical, chemical, and biological properties of soil while reducing environmental impacts by 15–45% compared to synthetic alternatives. Advanced biological treatment technologies, including anaerobic digestion, vermicomposting, and biochar production, achieve nutrient recovery efficiencies of 60–95% in diverse waste streams. Market analysis reveals a rapidly expanding sector projected to grow from $2.53 billion (2024) to $6.3 billion by 2032, driven by regulatory support and circular economy policies. Critical research gaps remain in standardisation, long-term performance evaluation, and integration with precision agriculture systems. Future developments should focus on AI-driven optimisation, climate-adaptive formulations, and nanobioconjugate technologies.