The aim of this study was to present optimized device-specific low-dose cone-beam computed tomography (CBCT) protocols with sufficient image quality for pre-surgical diagnostics and three-dimensional (3D) modelling of cleft defects. Six paediatric skulls were acquired, and an artificial bony cleft was created. A high-resolution CBCT scan acted as a reference standard (Accuitomo 170, Morita, Kyoto, Japan) for comparing eight low-dose protocols of Newtom VGi-evo (QR Verona, Cefla, Verona, Italy), which included Eco and Regular protocols with different field of views (FOVs). Delineation of lamina dura, cementoenamel junction (CEJ), trabecular bone and bony bridge were assessed. A 3D model of the defect was also evaluated. The dose area product of low-dose protocols ranged from 31 to 254 mGy*cm2. Despite the dose difference of up to eight times between applied protocols, trabecular bone and CEJ exhibited appropriate image quality in all scans. However, Regular small FOV protocols (5 × 5 and 8 × 5 cm2), for both lamina dura and bony bridge, demonstrated a significant improvement in image quality compared to Eco FOV counterparts. Based on 3D defect analysis, no significant difference existed between low-dose protocols and the reference standard. The findings highlight the possibility of achieving a considerable reduction (up to eight times) in the radiation dose using low-dose CBCT protocols while maintaining sufficient image quality for assessing anatomical structures and 3D modelling in cleft cases.