Purpose: Several parameters have been described for determining the success or failure of dental implants. The surface properties of transgingival implant components have had a great impact on the long-term success of dental implants. The purpose of this study was to compare the tendency of two periodontal pathogens to adhere to and colonize zirconia abutments and titanium alloys both in hard surfaces and soft tissues. Methods: Twelve patients participated in this study. Three months after implant placement, the abutments were connected. Five weeks following the abutment connections, the abutments were removed, probing depth measurements were recorded, and gingival biopsies were performed. The abutments and gingival biopsies taken from the buccal gingiva were analyzed using real-time polymerase chain reaction to compare the DNA copy numbers of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and total bacteria. The surface free energy of the abutments was calculated using the sessile water drop method before replacement. Data analyses used the Mann Whitney U-test, and P-values below 0.05 find statistical significance. Results: The present study showed no statistically significant differences between the DNA copy numbers of A. actinomycetemcomitans, P. gingivalis, and total bacteria for both the titanium and zirconia abutments and the biopsies taken from their buccal gingiva. The differences between the free surface energy of the abutments had no influence on the microbiological findings. Conclusions: Zirconia surfaces have comparable properties to titanium alloy surfaces and may be suitable and safe materials for the long-term success of dental implants.