This in vitro study aimed to assess the presence of microgaps at the implant–abutment interface in monolithic zirconia partial implant-supported fixed prostheses on transepithelial abutments versus Ti-base abutments. Methods: Sixty conical connection dental implants were divided into two groups (n = 30). The control group consisted of three-unit bridge monolithic zirconia connected to two implants by a transepithelial abutment. The test group consisted of monolithic zirconia three-unit restoration connected to two implants directly by a titanium base (Ti-base) abutment. The sample was subjected to thermocycling (10,000 cycles at 5 °C to 55 °C, dwelling time 50 s) and chewing simulation (300,000 cycles, under 200 N at frequencies of 2 Hz, at a 30° angle). The microgap was evaluated at six points (mesiobuccal, buccal, distobuccal, mesiolingual, lingual, and distolingual) of each implant–abutment interface by using a scanning electron microscope (SEM). The data were analyzed using the Mann–Whitney U tests (p > 0.05). Results: The SEM analysis showed a smaller microgap at the implant–abutment interface in the control group (0.270 μm) than in the test group (3.902 μm). Statistically significant differences were observed between both groups (p < 0.05). Conclusions: The use or not of transepithelial abutments affects the microgap size. The transepithelial abutments group presented lower microgap values at the interface with the implant than the Ti-base group in monolithic zirconia partial implant-supported fixed prostheses. However, both groups had microgap values within the clinically acceptable range.