Responding to the ever-growing concern about safe foods and security, the food industries are forced to seek an emerging technology capable of detecting and quantifying contaminations, especially those of biological origin. Among the different emerging technologies, hyperspectral imaging is considered a good alternative as it can be easily applied at all steps of the food production process and is a non-destructive technique. This paper reviews targeted analytical applications of hyperspectral imaging in monitoring biological contaminants in food. First, traditional techniques for detection of biological contaminants in foods are presented, where disadvantages for practical applications are highlighted and explained in detail. Second, prominent applications of hyperspectral imaging from the last decade to food safety and quality assessment are reviewed, specifically focusing on both deteriorative and pathogenic microorganisms, microbial toxins, and parasites; whether acting individually or collectively in spoiling food products and/or represent a health risk to the consumers. Finally, relevant current and future challenges, advantages and disadvantages of hyperspectral imaging applications are briefly examined.