The present study was carried out to compare the differences in contact, height and contact area between the implant-abutment interface and the implant-healing cap interface of an implant system featuring a locking tapered connection by using X-ray micro-tomography. It was also conducted to test in vitro whether the implant-healing cap tapered interface is capable of preventing bacterial leakage from the implant well to the external environment. The images of the samples, acquired by the X-ray micro-tomography, after being processed with a dedicated software, showed a greater contact height (CH) in the implant-abutment sample (3.57 mm) compared to the implant-healing cap sample (2.52 mm). This was also true for the contact area that was equal to 40.63 mm2 in the implant-abutment sample and 25.14 mm2 in the implant-healing cap sample. No bacteria were detected both in the nutrient of the test group and of the negative control after 24 h. An increased contact height and contact area in a tapered connection, between the implant and the abutment, have demonstrated to offer mechanical and biological advantages, in a implant-healing cap tapered connection. The major concern regards the microbiological aspects of this connection. The implant-healing cap tapered connection provides an hermetic barrier to microbial passage in vitro, even though such connection features lower contact height and contact area compared to the implant-abutment connection of the same implant system.