Abstract Objective. Cone-beam computed tomography is becoming more and more popular in applications such as 3D dental imaging. Iterative methods compared to the standard Feldkamp algorithm have shown improvements in image quality of reconstruction of low-dose acquired data despite their long computing time. An interesting aspect of iterative methods is their ability to include prior information such as sparsity-constraint. While a large panel of optimization algorithms along with their adaptation to tomographic problems are available, they are mainly studied on 2D parallel or fan-beam data. The issues raised by 3D CBCT and moreover by truncated projections are still poorly understood. Approach. We compare different carefully designed optimization schemes in the context of realistic 3D dental imaging. Besides some known algorithms, SIRT-TV and MLEM, we investigate the primal-dual hybrid gradient (PDHG) approach and a newly proposed MLEM-TV optimizer. The last one is alternating EM steps and TV-denoising, combination not yet investigated for CBCT. Experiments are performed on both simulated data from a 3D jaw phantom and data acquired with a dental clinical scanner. Main results. With some adaptations to the specificities of CBCT operators, PDHG and MLEM-TV algorithms provide the best reconstruction quality. These results were obtained by comparing the full-dose image with a low-dose image and an ultra low-dose image. Significance. The convergence speed of the original iterative methods is hampered by the conical geometry and significantly reduced compared to parallel geometries. We promote the pre-conditioned version of PDHG and we propose a pre-conditioned version of the MLEM-TV algorithm. To the best of our knowledge, this is the first time PDHG and convergent MLEM-TV algorithms are evaluated on experimental dental CBCT data, where constraints such as projection truncation and presence of metal have to be jointly overcome.