Little has been studied about microclimate and the thermal comfort during the implementation of silvopastoral systems. This study aimed to evaluate the microclimate and thermal comfort during the implementation of High Biodiversity Silvopastoral System with Nuclei (SPSnu). Three treatments were investigated, SPSnu with 5 and 10% of the pasture area with nuclei, (SPSnu5 and SPSnu10, respectively), and treeless pasture (TLP). Each treatment was subdivided into 4 areas: within the nuclei, around the nuclei, around the nuclei with shade and internuclei. The analyzed variables were soil surface temperature, air temperature, wind speed, relative humidity, black globe temperature and the Heat Load Index (HLI) at 20 and 120 cm height. We hypothesized that the wind speed reduction associated with insufficient shade projection typical of the first years of SPSs may interfere in microclimate and thermal comfort during the hot seasons. SPSnu5 and SPSnu10 had a reduction in wind speed of 51.58% and 68.47% respectively when compared to TLP at 20 cm. Soil surface temperature and air temperature at 120 cm were higher for SPSnu than TLP. The same effect was observed for the HLI. At 20 cm, HLI indicated better thermal comfort in TLP than in the SPSnu treatments. The lack of shade projection from young nuclei in conjunction with the decrease of wind speed between the nuclei caused a higher air temperature and HLI in the SPSnu treatments, we called this conditions, windbreak countereffect. Farmers must knowledge this effect when implementing SPSs, and when necessary, mitigate with the proper management decisions.