Background and Objectives: Infections and capsular contractures remain unresolved issues in implant-based breast reconstruction. Capsular contractures are thought to be caused by the endogenous flora of the nipple duct. However, little is known about the antibiotic susceptibility of the microorganisms involved. This study aimed to evaluate the composition of endogenous breast flora and its antimicrobial susceptibility in patients with breast cancer. This study will aid in selecting a prophylactic antibiotic regimen for breast reconstruction surgery. Materials and Methods: We obtained bacteriologic swabs from the nipple intraoperatively in patients who underwent implant-based breast reconstruction following nipple-sparing mastectomy between January 2019 and August 2021. Antibiotic susceptibility tests were performed according to the isolated bacteriology. Statistical analysis was performed based on several patient variables to identify which factors influence the antibiotic resistance rate of endogenous flora. Results: A total of 125 of 220 patients had positive results, of which 106 had positive culture results for coagulase-negative Staphylococcus species (CoNS). Among these 106 patients, 50 (47%) were found to have methicillin-resistant staphylococci, and 56 (53%) were found to have methicillin-susceptible staphylococci. The methicillin resistance rate in the neoadjuvant chemotherapy group (56.3%) was significantly higher (OR, 2.3; p = 0.039) than that in the non-neoadjuvant chemotherapy group (35.5%). Conclusions: Based on the results, demonstrating high and rising incidence of methicillin-resistant staphylococci of nipple endogenous flora in patients with breast cancer compared to the past, it is necessary to consider the selection of prophylactic antibiotics to reduce infections and capsular contracture after implant-based breast reconstruction.