Obesity is a frequent comorbidity among patients undergoing cardiac surgery with cardiopulmonary bypass (CPB). Cardiac surgery with CPB impairs microcirculatory perfusion, which is associated with multiple organ failure. As microvascular function is frequently compromised in obese patients, we studied whether cardiac surgery with CPB has a more detrimental effect on microcirculatory perfusion in obese patients. Sublingual microcirculatory perfusion was measured with sidestream dark field (SDF) imaging in obese patients (body mass index ≥32 kg/m2; n = 14) without type II diabetes mellitus and in lean patients (BMI 20–25 kg/m2; n = 22) undergoing cardiac surgery with CPB. CPB reduced systolic blood pressure and mean arterial pressure more profoundly in lean compared with obese patients (SBP: 38% vs. 18%; MAP: 11% vs. 8%, p < 0.05), and both restored after weaning from CPB. No differences were present in intraoperative glucose, hematocrit, hemoglobin, lactate, and blood gas values between obese and lean patients. Microcirculatory perfusion did not differ between obese and lean patients the day before surgery. CPB decreased microcirculatory perfusion with 9% in both groups, but this was only significant in lean patients (p < 0.05). Three days following surgery, microcirculatory perfusion was restored in both groups. In conclusion, microcirculatory perfusion was equally disturbed during cardiac surgery with CPB in metabolically healthy obese patients compared to lean patients.