Objectives: To evaluate the influence of the level of three micro-CT reconstruction tools: beam-hardening correction (BHC), smoothing filter (SF), and ring artefact correction (RAC) on the fractal dimension (FD) analysis of trabecular bone. Methods: Five Wistar rats’ maxillae were individually scanned in a SkyScan 1174 micro-CT device, under the following settings: 50 kV, 800 µA, 10.2 µm voxel size, 0.5 mm Al filter, rotation step 0.5°, two frames average, 180° rotation and scan time of 35 min. The raw images were reconstructed under the standard protocol (SP) recommended by the manufacturer, a protocol without any artefact correction tools (P0) and 35 additional protocols with different combinations of SF, RAC and BHC levels. The same volume of interest was established in all reconstructions for each maxilla and the FD was calculated using the Kolmogorov (box counting) method. One-way ANOVA with Dunnet’s post-hoc test was used to compare the FD of each reconstruction protocol (P0–P35) with the SP (α = 5%). Multiple linear regression verified the dependency of reconstruction tools in FD. Results: Overall, FD values are not dependent on RAC (p = 0.965), but increased significantly when the level of BHC and SF increased (p < 0.001). FD values from protocols with BHC at 45% combined with SF of 2, and BHC at 30% combined with SF of 4 or 6 had no statistical difference compared to SP. Conclusions: BHC and SF tools affect the FD values of micro-CT images of the trabecular bone. Therefore, these reconstruction parameters should be standardized when the FD is analyzed.