The purpose of this finite element analysis (FEA) was to evaluate the stress distribution within the prosthetic components and bone in relation to varying cement thicknesses (from 20 to 60 μm) utilized to attach a zirconia crown on a conometric cap. The study focused on two types of implants (Cyroth and TAC, AoN Implants, Grisignano di Zocco, Italy) featuring a Morse cone connection. Detailed three-dimensional (3D) models were developed to represent the bone structure (cortical and trabecular) and the prosthetic components, including the crown, cement, cap, abutment, and the implant. Both implants were placed 1.5 mm subcrestally and subjected to a 200 N load at a 45° inclination on the crown. The results indicated that an increase in cement thickness led to a reduction in von Mises stress on the cortical bone for both Cyroth and TAC implants, while the decrease in stress on the trabecular bone (apical zone) was relatively less pronounced. However, the TAC implant exhibited a higher stress field in the apical area compared to the Cyroth implant. In summary, this study investigated the influence of cement thickness on stress transmission across prosthetic components and peri-implant tissues through FEA analysis, emphasizing that the 60 μm cement layer demonstrated higher stress values approaching the material strength limit.