Background <p>Hidradenitis suppurativa (HS) is an inflammatory skin disease characterized by painful nodules, abscesses, and sinus tract formation. While dysbiosis of the skin microbiome has been implicated in HS pathogenesis, most studies focus on surface flora, leaving the microbial composition of deep tissue lesions poorly characterized, particularly in surgically managed Hurley stage III disease. This study investigates the culture-based subcutaneous microbiome of stage III HS requiring surgical intervention, with the goal of identifying microbial patterns and their associations with patient-specific clinical features.</p> Methods <p>A retrospective chart review of 83 patients undergoing surgical excision for HS was performed. Intraoperative subcutaneous tissue samples were cultured under aerobic and anaerobic conditions. Demographic, clinical, and treatment data were analyzed for associations with microbial findings.</p> Results <p><i>Streptococcus</i> species and <i>Bacteroides</i> were significantly associated with a history of type 2 diabetes mellitus (T2DM) (<i>p</i> &lt; 0.001 and <i>p</i> = 0.009, respectively). Patients without steroid use within 90 days of culture had lower odds of having an obligate anaerobe present (<i>p</i> = 0.041). Patients without T2DM were less likely to have a facultative anaerobe present (<i>p</i> = 0.031). Microbial profiles did not vary significantly by anatomical site.</p> Conclusions <p>The subcutaneous microbiome in stage III HS remains poorly characterized due to the historical focus on surface lesions and non-surgical populations. Our findings highlight distinct microbial profiles within deep tissue that are influenced by comorbidities and steroid use. Plastic and reconstructive surgeons have a critical role in managing advanced HS. This study provides evidence of the subcutaneous microbiome composition that may be used to tailor perioperative antibiotics based on the surgeon’s expertise and clinical factors.</p>