Obesity is known to be associated with high complication rates. The aim of this study was to evaluate the effect of bilateral procedures on complication rates in obese patients undergoing autologous breast reconstruction with deep inferior epigastric perforator flaps. Medical records of patients undergoing autologous breast reconstruction between January 2017 and December 2019 were retrospectively reviewed. Patients were divided into two groups according to their body mass index (BMI): Group 1 (BMI > 30) and Group 2 (BMI < 30). Group 1 was further divided into 3 subgroups: Group 1a (bilateral reconstruction), Group 1b (unilateral reconstruction), and Group 1c (unilateral reconstruction and contralateral symmetrization). Outcomes and complication rates were compared between groups. Ninety-one patients (with 119 free flaps) were followed up between 6 and 12months. Length of hospital stay, smoking rates, and age were similar in all groups. Group 1 had significantly more rates of wound dehiscence (p = 0.024), mastectomy skin flap necrosis (p = 0.019), and re-operation (p = 0.033). The operation time was significantly higher in group 1 (p = 0.003). There was no significant difference between group 1 and group 2 in terms of hematoma-seroma formation, flap loss, and pulmonary thromboembolism rates. When obese subgroups were compared, no significant difference was observed in terms of complications. In our series, microvascular breast reconstruction was associated with more complication rates in obese patients. However, bilateral procedures in the obese patient group did not significantly increase risk of complications as compared to unilateral procedures. By taking appropriate measures bilateral procedures can be performed in obese patients without additional risks.