The autotempering phenomenon and carbon partitioning from bainitic subunits during the bainite transformation suggest that the tempering behavior of the nanostructured bainite may be different compared to that of martensite. This article aims to investigate the thermal stability of the microstructure in two low alloy nanostructured bainitic steels containing 0.89 wt% carbon content. Nanostructured bainite was obtained after austempering at 250 °C for optimum heat treatment time. Nanostructured bainitic steels were tempered at the temperature range of 300–700 °C for 30 min. Additionally, the effect of prolonged austempering beyond the optimum heat treatment condition at austempering temperature was studied. Microstructural characteristics were evaluated using optical and field emission gun scanning electron microscopes and X-ray diffraction methods. Hardness variations during tempering of nanostructured bainite compared with that of martensite microstructure obtained in the same primary steels after austenitizing and quenching. Results indicated that microstructural characteristics of nanostructure bainite didn’t change significantly at heat treatment times longer than that needed for bainite transformation completion at isothermal bainite heat treatment temperature. Moreover, results approved the higher tempering resistance of nanostructured bainite compared to that of martensite in the same steel. It has been shown that tempering the nanostructured bainite up to 400 °C didn’t change the microstructure and hardness, while the changes were pronounced at higher tempering temperatures. It has been suggested that cementite precipitation was more significant when a higher number of dislocations were present in nanostructured bainite before starting the tempering process.