<p>The medicinal and aromatic plants (MAPs) offer a wide range of remedies for various health conditions, owing to the presence of distinctive secondary metabolites, such as phenolics, alkaloids, saponins, terpenes, flavonoids, glycosides, and essential oils. Diverse microbial communities associated with MAPs, whether mutualistic, symbiotic, or neutral, substantially influence plant growth and development, thereby determining the quality and quantity of secondary metabolite production.The advent of metagenomics and other omics-based approaches has greatly advanced our understanding of the intricate interactions between medicinal and aromatic plants and their associated microbiomes. As a result, these approaches enable the characterization of microbial diversity, community composition, metabolic functions, and the discovery of novel taxa, along with insights into their physiological and biochemical attributes. Although numerous comprehensive reviews have addressed the applications of metagenomics in food crops, similar studies focusing on MAPs remain limited. This narrative review aims to examine the beneficial effects of plant–microbe associations in MAPs, with particular emphasis on their physiological impacts, including secondary metabolite production, induction of resistance, environmental adaptation, nutrient uptake, and phytohormone regulation. Such interactions hold considerable potential for enhancing key physiological traits, including biomass accumulation, essential oil yield, secondary metabolite production, and stress tolerance in economically important crops. Beyond advancing sustainable and eco-friendly agricultural practices, these approaches also hold significant potential for applications in medicine and biotechnology.</p>