Background The reference protocol for the quantification of coronary artery calcium (CAC) should be updated to meet the standards of modern imaging techniques. Purpose To assess the influence of filtered-back projection (FBP), hybrid iterative reconstruction (IR), and three levels of deep learning reconstruction (DLR) on CAC quantification on both in vitro and in vivo studies. Material and Methods In vitro study was performed with a multipurpose anthropomorphic chest phantom and small pieces of bones. The real volume of each piece was measured using the water displacement method. In the in vivo study, 100 patients (84 men; mean age = 71.2 ± 8.7 years) underwent CAC scoring with a tube voltage of 120 kVp and image thickness of 3 mm. The image reconstruction was done with FBP, hybrid IR, and three levels of DLR including mild (DLRmild), standard (DLRstd), and strong (DLRstr). Results In the in vitro study, the calcium volume was equivalent ( P = 0.949) among FBP, hybrid IR, DLRmild, DLRstd, and DLRstr. In the in vivo study, the image noise was significantly lower in images that used DLRstr-based reconstruction, when compared images other reconstructions ( P < 0.001). There were no significant differences in the calcium volume ( P = 0.987) and Agatston score ( P = 0.991) among FBP, hybrid IR, DLRmild, DLRstd, and DLRstr. The highest overall agreement of Agatston scores was found in the DLR groups (98%) and hybrid IR (95%) when compared to standard FBP reconstruction. Conclusion The DLRstr presented the lowest bias of agreement in the Agatston scores and is recommended for the accurate quantification of CAC.