Technological interventions have been the dominant framing of sustainable food innovation in Sub-Saharan Africa, often neglecting the sociocultural and knowledge systems that influence the production, processing, and consumption of food. This study re-conceptualizes food innovation through a product and process lens and emphasizes the role of gendered Indigenous knowledge systems in shaping the diversity of food products and the methods through which they are produced and processed. This study, based on a systematic literature review (2020–2025), shows that gender relations and Indigenous knowledge systems (IKS) are key drivers of product innovation (e.g., climate-resilient crops, diversified diets, and traditional food products) and process innovation (e.g., fermentation, agroecological production, preservation, and water and soil management practices). The findings show that women are at the forefront of both domains, especially in food processing and value addition, where indigenous knowledge creates adaptive and context-specific innovation. However, structural inequalities continue to hinder their ability to scale up these innovations in the sector. This study introduces a Gendered Indigenous Innovation Framework (GIIF) to conceptualize the co-evolution of product and process innovations in socio-cultural, economic, and environmental systems. Evidence shows that the integration of gender-responsive and Indigenous knowledge-based approaches enhances food quality, reduces post-harvest loss, improves climate resilience, and strengthens sustainable livelihoods. The study concludes that African food systems must shift away from technocentric models towards endogenous and inclusive innovation systems that recognize locally embedded product and process innovations.