Implant–abutment connection (IAC) is a key factor for the long-term success and stability of implant-supported prosthodontic restoration and its surrounding tissues. Misfit between prosthodontic abutment and implant at the IAC leads to technical and biological complications. Two kinds of prosthodontic abutments are currently available on the market: original and third-party abutments. The aim of this pilot study was to test and compare the internal fit (gap) at the implant–abutment interface depending on the abutment fabrication method based on microbial leakage in static conditions and the need for the use of gap sealing material. Two groups of 40 implants were formed on the basis of the type of abutment. In each of the groups of two implant systems, two subgroups of 10 implants were formed. The tested subgroups consisted of 10 implants with sealing material and a negative control subgroups consisting of 10 implants without any sealing material. The test material, GapSeal (Hager and Werken, Duisburg, Germany) was applied in the test subgroups. The implant–abutment assemblies were contaminated with a solution containing Staphylococcus aureus and Candida albicans for 14 days under aerobic conditions. Results showed that there was no statistically significant difference regarding the microbial leakage between the original and third-party custom-made abutments, regardless of the use of sealing material. It can be concluded that the abutment fabrication method has no significant influence on sealing efficacy regarding the bacterial and fungal leakage in static conditions.