To evaluate the influence of artefacts generated by titanium and zirconium implants on trabecular bone architecture assessment through cone-beam CT (CBCT). The influence of kilovoltage (kVp) and metal artefact reduction (MAR) in such analysis was also assessed. CBCT scans were obtained with Picasso Trio with or without a titanium or zirconium implants in a posterior region of a mandible using 70, 80 or 90 kVp, with or without MAR. The other acquisition settings were constant: field of view 8 × 5 cm, voxel size 0.2 mm, 5 mA, 24 s and 720 frames. Two volumes of interest (VOIs) were determined comprising trabecular bone mesial and distal to the implant area. The following morphometric parameters were measured: connectivity density (Conn. Dn.), fractal dimension (FD), bone volume fraction (BV/TV), bone surface density (BS/TV), trabecular thickness (Tb. Th.), and trabecular spacing (Tb. Sp.), and compared by multiway ANOVA (α = 0.05). For Conn. Dn. and FD, with MAR, the zirconium group showed values significantly lower than the other groups (p < 0.05). For BV/TV, BS/TV, Tb. Th. and Tb. Sp., the zirconium group showed the highest values, regardless of MAR condition (p < 0.05). MAR increased BS/TV and Tb. Th. values, and decreased FD values for zirconium group. In general, the kVp level did not influence trabecular morphometric parameters. The assessment of the trabecular bone architecture was mainly influenced by the expression of the artefacts generated by zirconium implants. MAR decreased the FD and increased the BS/TV and Tb.Th. values regardless of the kVp level.