The bioprospecting of lotus seeds has a promising future as an alternative protein supplement and potential pharmaceutical source. Because there are no detailed reports on the toxic effects of long-term consumption of lotus seeds and their products, more research is needed. Although the nutraceutical value of lotus seeds has been established, more precise exploration of value-added compounds may be beneficial in health promotion. Lotus seeds, like other edible seeds, are vulnerable to microbial contamination and spoilage. Contaminant and spoilage microflora (bacteria and fungi), their toxins, and control measures will help to popularise the use of lotus seeds. Because lotus seeds have potential nutraceutical benefits, combining their flour with other nutritionally dense legumes (e.g., soybean) or millets (e.g., finger millet) will be extremely beneficial in developing low-cost proteinaceous and health food supplements to combat malnutrition and specific ailment.