The relationship between bacterial infiltration and internal conical Implant-Abutment Interfaces (IAIs) with different conicities still requires investigations that can offer valuable information in the clinical understanding of peri-implant health. The present study aimed to verify the bacterial infiltration of two internal conical connections with an angulation of 11.5° and 16° with the external hexagonal connection as a comparative after thermomechanical cycling using saliva as a contaminant. Test (n = 10) and control (n = 3) groups were set up. Evaluations were made on torque loss, Scanning Electron Microscopy (SEM), and Micro Computerized Tomography (MicroCT) after performing 2 × 10 mechanical cycles (120 N) and 600 thermal cycles (5°-55° C) with 2 mm lateral displacement. The contents of the IAI were collected for microbiological analysis. There was a difference ( < 0.05) in torque loss of the groups tested; groups from the 16° IAI obtained a lower percentage of torque loss. All groups presented contamination and the analysis of the results shows that the microbiological profile of the IAI differs qualitatively from the profile found in the saliva used for contamination. The mechanical loading affects the microbiological profile found in the IAIs ( < 0.05). In conclusion, the IAI environment may favor a microbiological profile different from that of saliva and the thermocycling condition may alter the microbial profile found in the IAI.