The optimal thermal environment for sick preterm infants is unknown. Incubator temperature can be regulated to an abdominal wall temperature of 36.5°C [neutral temperature (NT)] or to a minimal temperature difference (<2°C) between abdominal wall and extremities [comfort temperature (CT)]. This could affect the microcirculation, particularly in infants with impaired perfusion. We assessed the microvascular perfusion with near-infrared photoplethysmography (NIRP) at these two target temperatures between d 1 and 4 of life in preterm infants with normal (NL group) or impaired (RED group) microcirculation as determined by a clinical score. Signal strength variables such as area under the curve (AUC) and the first derivate of the amplitude (FLUX) were calculated. Starting temperature was randomized to NT or to CT and then followed by the other temperature. A significant increase of FLUX and AUC in the RED group was found with NT as starting temperature (FLUX: 282 ± 76 at NT versus 627 ± 211 at CT; p = 0.025; AUC: 73 ± 47 at NT versus 234 ± 112 at CT; p = 0.009), but not with CT. In NL infants, both parameters did not change significantly. Increasing the incubator temperature to CT changes thermoregulatory flow to the extremities in preterm infants with impaired microvascular perfusion and might improve tissue flow.