There is a paucity of studies aimed to compare the healing process of piezosurgery with conventional surgery. This study evaluated the histopathological assessment of healing process in osteotomy defects caused by these surgical methods in rats using an amniotic membrane (hAM). In this randomized controlled experimental study, there were 2 main groups: group 1 (Piezosurgery method-right tibia) and group 2 (Conventional surgery method-left tibia) and subgroups determined by the sacrification periods on the 7th (n = 20) and 21st days (n = 20). hAM was used in all groups. The primary outcome variable was new bone formation, while inflammation, necrosis, fibrotic tissue formation in the defective zone were secondary outcomes. 40 male Sprague Dawley rats were used. The 7th day fibrosis levels and the 7th new bone-building level of the group who underwent piezosurgery were found to be significantly higher than those of the group undergoing conventional surgery (p < 0.05) and the 21st new bone-building level was significantly lower than conventional surgery. In all rats, on the 21st day, there were statistically significant decreases in inflammation, fibrosis, and increases in the healing score (p < 0.05). Also, there was no statistically difference in new bone formation between 7st and 21st days (p > 0.05). The choice of conventional surgery when applying with hAM increases the new bone building in the late period.