This study aimed to assess the biomechanical behavior of endocrown-restored mandibular molars according to “margin design” and “coverage extent” using finite element analysis (FEA). Six 3D solid models were fabricated, namely, those with complete occlusal coverage: A (butt joint), B (anatomic margin); partial coverage (two mesial cusps): C (butt joint), D (anatomic margin); and partial coverage with mesial class II cavity: E (butt joint), F (anatomic margin). All models received lithium disilicate endocrowns (2.0 mm thickness and 4.0 mm central retainer cavity depth). A 300 N vertical load was applied to the occlusal surface, while a 250 N oblique load was applied at 45° to the lingual inclined planes of the buccal cusps. The maximum von Mises stress (VMS) distribution patterns were calculated for the endocrown, tooth structure, and cement layer. The VMS on the prepared teeth and cement layer showed subtle differences between the tested models under vertical loads. The anatomic margin (partial and complete coverage) exhibited a more homogeneous stress distribution and offered a more adhesive area of the tooth structure. Under oblique loading, the anatomic margin (complete and partial), except Model D, exhibited the lowest VMS in the cement layer. An anatomically based endocrown could be a promising alternative to the butt joint design, providing better-devised endocrown restorations, which could potentially yield a more benign stress dissipation.