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The world food systems are facing the fundamental challenges that are being necessitated by climatic changes, increasing population count, protein demand and the escalating non-communicable diseases. Ecological nutrition approaches should therefore be concerned with ecological stability and functional health outcomes. The South Indian traditional medicine is Siddha medicine, an ancient system that provides a constitution-based dietary system that focuses on the three humours, i.e., Vatham, Pitham and Kabam, and the concept of food as medicine. In line with this, other proteins, such as plant-based, microbial and insect-derived proteins and cultivated proteins, have also become viable options to minimise the environmental impact of traditional livestock production and satisfy the human protein needs. This review explains how the bridging of Siddha nutrition philosophy and current alternative-protein innovation can be affected to suggest a unified and sustainable mix of food. It also critically reviews the Siddha dietary categories, methods of digestive improvement, fermentation and detoxification methods, and how they correlate to the bioavailability, digestibility, and activity of other proteins. The sustainability of the environment is determined in terms of Siddha ecological ethics and the life-cycle assessment of alternative protein systems. The issues of safety, allergenicity, cultural acceptance, and the regulatory viewpoints are also considered in favour of the support of translational applicability. Lastly, the review provides future research directions such as personalized nutrition based on constitutions, integrative clinical validation models, and the innovation strategies of functional foods. Applying the Siddha wisdom to the other protein science provides a culturally based, ecologically sustainable and functional-driven concept that can be used to achieve sustainable food transitions and enhance global health outcomes.