Background This study aimed to evaluate the effect of virtual cement space and restorative materials on the fit of computer-aided design and computer-aided manufacturing (CAD-CAM) endocrowns. Methods A mandibular first molar tooth model received a butt joint margin endocrown preparation with a 2-mm occlusal thickness. Then, using a 3D-printing system, 120 copies of this prepared die were printed and assigned equally to three groups with different cement space settings (30, 60, and 120 μm) during the chairside CAD design. In the milling process, CAD-based models with a particular space setting were subdivided into four groups (n = 10) and fabricated from different CAD-CAM materials: Vita Suprinity (VS), Celtra Duo (CD), Lava Ultimate (LU), and Grandio blocs (GR). Finally, the endocrowns were stabilized over their corresponding models with siloxane and subjected to micro-computed tomography to measure the fit. Results The cement space that was predesigned at 30 μm generated the largest marginal discrepancy (from 144.68 ± 22.43 μm to 174.36 ± 22.78 μm), which was significantly different from those at 60 μm and 120 μm (p < 0.001). The combination of VS or CD with a pre-setting cement space of 60 μm and the combination of LU or GR with a cement space of 120 μm showed better agreement between the predesigned and actual measured marginal gap widths. For internal adaptation, only the cement space set to 30 μm exceeded the clinically acceptable threshold (200 μm). Conclusions The setting of the cement space and restorative material significantly affected the marginal adaptation of CAD-CAM endocrown restorations. Considering the discrepancy between design and reality, different virtual cement spaces should be applied to ceramic and resin composite materials.