Inflammatory diseases affecting the soft and hard tissues surrounding an implant represent a new challenge in contemporary implant dentistry. Among several methods proposed for the decontamination of titanium surfaces, the administration of topical 14% doxycycline gel seems to be a reliable option. In the present study, we evaluated the microbial effect of 14% doxycycline gel applied on titanium surfaces and exposed to human salivary microbes in anaerobic conditions. We also examined the composition of the exposed surfaces to assess the safe use of periodontal gel on titanium surfaces. Six anatase and six type 5 alloy titanium surfaces were used and divided into two groups: The test group and the positive control group. Both were cultured with human salivary samples in anaerobic conditions. On the test groups, 240 mg of periodontal gel was applied. The microbial assessment was performed with a colony-forming unit (CFU) count and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) to identify the species. The surface integrity was assessed using scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDS). The results demonstrated the microbial efficacy of the 14% doxycycline periodontal gel and its safe use on titanium surfaces. However, the SEM observations revealed the permanence of the gel on the titanium surfaces due to the physical composition of the gel. This permanence needs to be further investigated in vivo and a final polishing protocol on the titanium surface is recommended.