The generation alpha is going to face a red alert on the verge of drug resistance and limited efficacies of most of the popular drugs used until today. Driven the fact, the pharmaceutical industries have already started the re-orientation of pharmaceutics targeting the possibilities of unconventional therapeutics. Nutraceuticals, the chimera of nutrition and pharmaceuticals, have caught the limelight of present consideration although their use is not de novo. Many age-old civilizations have recorded proof of the disease-modifying ability of various food ingredients. Having pace with the faster-growing market for nutraceuticals, the nanocarrier-mediated deliveries and production of solid-lipid nanoparticles, emulsions, liposomes, nanostructured lipid carriers, self-dispersing lipid formulations, biopolymer-based delivery systems, and nanolaminated systems embedding nutraceuticals are given foremost priorities nowadays. Usually, the role of microbes is praised for the large-scale industrial production of some definite nutraceuticals. As a result, the quality control safety issues remain neglected. Therefore, to get the best use of nutraceuticals, the microbiological evaluations of nutraceutical and nanonutraceutical formulations are the high demand of the current era. Here in this chapter, the microbiological assessments including broth dilution, spread plate, streak plate, and pour plate methods, and different culture media for detection of microbial contamination in nutraceutical formulations have been enlisted. In addition, the role of microorganisms in the production and storage of nutraceuticals has been discussed here. Further, a glimpse of the emerging tools and techniques of microbial assays and the future scope of improvisation are scribbled down.