Taxus wallichiana Zucc. (Himalayan yew) is a well-known medicinal plant of the Taxaceae family. The anticancer properties of Taxus species are well-known across the medical community. It was mentioned in the IUCN Red List a few years ago; therefore, it is crucial to protect and propagate the species. In this perspective, an understanding of the root microbiome with special reference to plant growth-promoting (PGP) activities is a prerequisite for developing rapid propagation approaches for this slow-growing plant species. In this context, T. wallichiana roots have recently been used to isolate beneficial bacteria and fungi. The isolated bacteria and fungi had genotypic and phenotypic traits of Burkholderia and Enterobacter, and Aspergillus and Penicillium species, respectively. Phosphate solubilization was demonstrated by all endophytes, as evidenced by the generation of phosphatases in a medium containing calcium, iron, and aluminum phosphate and phytases in a medium containing calcium and sodium phytate. Additionally, yellow pigment with antagonistic or antibacterial activity was generated by Burkholderia sp. Apart from their ability to promote plant development in vitro, the endophytic bacteria Burkholderia and Enterobacter had favorable effects on the growth of test plants under net house conditions. Additionally, endophytic fungi were capable of producing taxol and other highly significant secondary metabolites, i.e., phenols, fatty acids, aromatic dicarboxylic acid, and alkaloids in ethyl acetate extracts. Furthermore, both bacterial and fungal crude extracts and rich fractions showed antibacterial and antifungal activity, respectively. The capacity of these endophytic fungi to generate a range of secondary metabolites and their antimicrobial qualities are likely to have potential applications in biotechnological, medicinal, and agricultural domains.