In breast surgeries, a lactiferous duct leading to lactic glands of breast parenchyma allows direct contamination by normal bacterial flora of the nipple-areola complex. Complete blockage of nipple flora from the intraoperative field is almost impossible. We aimed to analyze the microbiological profile of nipple flora of breast cancer patients who underwent an implant-based immediate breast reconstruction after a total mastectomy, and to evaluate the association of nipple bacterial flora with postoperative complications. A retrospective chart review was performed of patients who underwent an implant-based immediate breast reconstruction after a total mastectomy. A nipple swab culture was performed preoperatively. Patient demographics, surgical characteristics, and complications were compared between positive and negative nipple swab culture groups. Microbiological profile data including antibacterial resistance were collected. Among 128 breasts, 60 cases (46.9%) had positive preoperative nipple swab culture results. Staphylococcus epidermidis accounted for 41.4% of microorganisms isolated. A multivariate logistic regression analysis of postoperative complications revealed that the presence of nipple bacterial flora was a risk factor for capsular contracture. Seven cases of postoperative infection were analyzed. In 2 cases (40% of pathogen-proven infection), the causative pathogen matched the patient's nipple bacterial flora, which was methicillin-resistant S. epidermidis in both cases. Nipple bacterial flora was associated with an increased risk of capsular contracture. Preoperative analysis of nipple bacterial flora can be an informative source for treating clinically diagnosed postoperative infections. More studies are needed to determine the effectiveness of active antibiotic decolonization of the nipple.