The aim of this study was to investigate the effect of thermogenic supplementation on the bone tissue of rats subjected to orthodontic movement. A total of 38 male Wistar rats underwent orthodontic movement of the left permanent maxillary first molars for 21 days. The rats were assigned to three groups: Control group: water; Thermogenic 1: C4 Beta Pump thermogenic; or Thermogenic 2: PRE-HD/Pre-workout. Micro-computed tomography (micro-CT) was used to investigate the dynamic changes in the microstructure of alveolar bone during orthodontic tooth movement in rats. Histopathologic analysis was performed by hematoxylin and eosin (H&E) staining, whereas tartrate-resistant acid phosphatase (TRAP) was employed for osteoclast count. Maxillary tissue was collected and evaluated by immunohistochemistry for receptor activator of NF-κB (RANK), receptor activator of NF-κB ligand (RANKL), and osteoprotegerin (OPG). The Thermogenic 2 group exhibited a significantly lower percentage of bone volume fraction (BV/TV) (68.21% ± 17.70%) compared to the control (86.84% + 12.91%) and Thermogenic 1 groups (86.84% + 15.94%) (p < 0.05). The control group had a significantly higher mean orthodontic movement in the mesial direction (0.2143 mm + 0.1513 mm) than the Thermogenic 2 group (0.0420 mm + 0.05215 mm) (p < 0.05). The Thermogenic 2 and Thermogenic 1 groups showed a stronger immunostaining for RANKL when compared to the control group (p < 0.05). The supplementation used in the Thermogenic 2 group (PRE-HD/Pre-workout) induced alveolar bone loss in rats subjected to orthodontic movement, which can be related to the regulation of the RANK/RANKL/OPG signaling pathway. This suggests the influence of thermogenic supplements on bone metabolism seems to depend on their composition.