Plenty of studies have explained the dynamics of plant–microbe interactions, their impact on plant growth, and the overall functioning of the plant ecosystem. Beneficial bacteria are crucial for improving crop production, managing biological diseases, and supporting plant stress resilience. Special emphasis is given to bacteria within the plant’s vascular system that provides a unique habitat, which supports endophytic growth. The study of vascular tissue’s unique microbial environment is gaining importance due to its potential role in protecting plants by inducing plant systemic resistance against pathogens. However, difficulties in isolating the bacteria residing in vascular tissue is a major challenge in the full exploration of these microbiomes. The employment of both traditional and advanced techniques, such as PCR-based 16S rRNA cloning and next-generation sequencing (NGS), can complement each other in advancing our knowledge of these bacterial communities.