The mechanisms involved in changes in energy metabolism caused by excessive exposure to fluoride (F) are not completely understood. The present study employed proteomic tools to investigate the molecular mechanisms underlying the dose- and time-dependency of the effects of F in the rat liver mitochondria. Thirty-six male Wistar rats received water containing 0, 15 or 50 mgF/L (as NaF) for 20 or 60 days. Rat liver mitochondria were isolated and the proteome profiles were examined using label-free quantitative nLC-MS/MS. PLGS software was used to detect changes in protein expression among the different groups. The bioinformatics analysis was done using the software CYTOSCAPE® 3.0.7 (Java®) with the aid of ClueGo plugin. The dose of 15 mgF/L, when administered for 20 days, reduced glycolysis, which was counterbalanced by an increase in other energetic pathways. At 60 days, however, an increase in all energy pathways was observed. On the other hand, the dose of 50 mgF/L, when administered for 20 days, reduced the enzymes involved in all energetic pathways, indicating a lower rate of energy production, with less generation of ROS and consequent reduction of antioxidant enzymes. However, when the 50 mgF/L dose was administered for 60 days, an increase in energy metabolism was seen but in general no changes were observed in the antioxidant enzymes. Except for the group treated with 50 mgF/L for 20 days, all the other groups had alterations in proteins in attempt to maintain calcium homeostasis and avoid apoptosis. The results suggest that the organism seems to adapt to the effects of F over time, activating pathways to reduce the toxicity of this ion. Ultimately, our findings corroborate the safety of the use of fluoride for caries control.