The human microbiome has emerged as a critical factor influencing surgical outcomes across a broad number of specialties. This paper explores the evolving interactions between the body’s microbiome and surgical practice, especially focusing on wound healing, post-operative recovery, and infection risk. We analyze current evidence from multiple surgical disciplines, including transplantation, reconstructive, bariatric, orthopedic, cardiothoracic, and oral surgery. Recognizing different microbial communities and their influence on surgical success opens doors to personalized medicine and targeted preventions. The studies discussed in this review provide valuable interdisciplinary insights that could ultimately uncover the microbiome’s fullest potential in optimizing future surgical protocols.