Microorganisms are known to be one of the cosmopolitan organisms mostly found in nature. Their presence in all forms of biotic and abiotic ecosystem showcase their immense potential in contaminating virtually most things found in nature. This review presents the insignificant roles played by microorganisms in the contamination of traditional herbal formulations sold in Nigeria, and also to showcase its detrimental health implications to human health. Before the introduction of modern medicine, Nigerians relied totally on herbs and other plant extracts for the treatment of different ailments. Presently, herbal medicine still remains popular due to its cultural acceptance, affordability, accessibility, and remedies to different types of health needs, ranging from pain relief, to immune support, gastrointestinal disorder, microbial diseases and digestive health effects. The contamination of herbal products in Nigeria by microbes occurs at different stages from the collection of plant extracts, processing, storage, up to distribution. Also, their formulations under non-sterile conditions, utilizing of contaminated water and improper handling by vendors also contributed to their contamination. The consumption of microbial contaminated herbs can cause health implications which can range from mild infections to life-threatening diseases. Also, the toxic metabolic byproducts produced by microbes in the herbs are highly pathogenic, which can lead to liver and kidney failure. To avoid these contaminations, proper hygiene and quality control measures should be implemented at all stages of herbal drug production. Also, Good Manufacturing Practices (GMP) including proper worker hygiene, and the usage of sterilized packaging tools should be employed during herbal formulations.