Prosthetic design is a critical step in implant treatment planning that must synchronize with implant positioning to promote a state of peri-implant health. Improperly designed prostheses may not only hinder patient (or professional) hygiene measures but also impact the ability of clinicians to examine the peri-implant supporting tissues for diagnostic purposes. The purpose of this review was to discuss the current state of the evidence surrounding prosthetic factors associated with peri-implant diseases. Following the chronologic order of implant treatment, key prosthetic variables were discussed in relation to peri-implant disease pathogenesis. Specific concepts including the impact of implant spatial positioning, abutment height, residual cement, and implant splinting were found to be associated with peri-implant disease pathogenesis. Excessive occlusal forces were found to play a role in susceptibility to prosthetic complications with limited evidence to suggest a role in peri-implant disease progression. An intimate prosthetic-biologic connection exists, which must be respected to promote an environment for long-term peri-implant stability and health.