Fungal mycotoxins from genera Aspergillus, Fusarium, and Penicillium contaminate feedstuff and food to induce serious health issues in humans and animals known as mycotoxicosis. Aspergillus, Penicillium, Alternaria, and Fusarium mycotoxins pose a serious threat to food quality and safety. Aflatoxins, zearalenone, ochratoxins, patulin, fumonisins, trichothecenes, deoxynivalenol have been documented to exert nephrotoxicity, immunotoxicity, hepatotoxicity, carcinogenicity, teratogenicity, and neurotoxicity in animals and humans. Implementation of HACCP-based procedures can mitigate mycotoxin-linked contamination whereas traditional methods (physical, biological, and chemical) could facilitate the decontamination process. However, the rising fungal resistance and conventional systems-associated challenges demand innovative strategies to rapidly eliminate mycotoxins without impacting the quality. The most important food-contaminating mycotoxins include liver-damaging aflatoxins; kidney-damaging ochratoxin A; cancer-causing, liver-damaging, and developmental defects-associated fumonisins; acute cardiac damage-related moniliformin; and gastroenteritis and immunotoxicity-associated zearalenone and deoxynivalenol. Therefore, mycotoxins can be categorized as teratogens, hepatotoxins, allergens, nephrotoxins, mutagens, neurotoxins, immunotoxins, and carcinogens. Mycotoxins are associated with various animal and human diseases including porcine pulmonary edema, Reye’s disease, Balkan endemic nephropathy, equine leuko-encephalomalacia, and alimentary toxic aleukia of humans. This study discusses the individual and combined impacts of foodborne fungal mycotoxins along with the related biochemical mechanisms and pathologies.