Sesame seeds (Sesamum indicatum L.) are globally valued for their rich nutritional profile, bioactive compounds, and functional food applications, but their safety is increasingly challenged by microbial contamination emerging at different stages of cultivation, harvesting, processing, and storage. Diverse microbial hazards—bacteria, fungi, and mycotoxin-producing species—compromise both food quality and consumer health, thereby undermining the economic potential of sesame-based functional foods. Contaminants such as Salmonella spp., Escherichia coli, Aspergillus flavus, and Penicillium species have been frequently reported in sesame supply chains, with documented cases of foodborne outbreaks linked to contaminated sesame products, highlighting the urgent need for improved microbial risk management. Functional food industries depend heavily on the consistent microbiological safety of plant-derived ingredients, and sesame seeds—despite their growing demand—remain vulnerable due to limited adoption of modern post-harvest handling technologies and inconsistent regulatory frameworks across producing regions.
This analytical overview synthesizes empirical evidence on the prevalence of microbial contaminants in sesame seeds, their pathways of entry, and their direct implications for functional food safety and public health. Special attention is given to the influence of environmental factors, inadequate drying, improper storage, and traditional processing practices that favor microbial proliferation. The paper further evaluates the extent to which current microbial control strategies—such as thermal treatments, irradiation, and sensor-based sorting—are effective in minimizing risks, while also identifying the limitations facing small-scale producers in adopting advanced technologies. The growing global interest in sesame-based nutraceuticals and fortified foods necessitates stricter standardization, continuous surveillance, and harmonized food safety protocols across the value chain. By consolidating existing findings, this overview aims to strengthen scientific understanding and support future innovations in microbial detection, prevention, and food safety assurance, ensuring that sesame seeds remain a reliable ingredient within functional food systems.