Peri-implantitis leads to bacterial contamination of titanium implant surfaces, potentially impairing the integrity of peri-implant tissues. This study investigated the effects of various decontamination strategies on contaminated titanium surfaces and their impact on gingiva-derived mesenchymal stem cells (GMSCs). Both rough and machined titanium surfaces were contaminated with bacteria and subsequently subjected to various mechanical and chemical decontamination methods. GMSC viability and osteogenic responses were analyzed to characterize cellular behavior on the treated surfaces. Cellular responses varied according to surface morphology. On rough surfaces, cell viability declined over time regardless of bacterial contamination or subsequent decontamination treatments. Conversely, machined surfaces supported increased cell viability in both decontaminated and uncontaminated groups, whereas viability remained unchanged on untreated contaminated surfaces. These findings suggest that effective bacterial decontamination of machined surfaces may promote GMSC proliferation and establish cellular conditions favorable for maintaining peri-implant tissue stability under controlled in vitro conditions. Correlation analyses demonstrated surface-dependent osteogenic responses. On rough surfaces, GMSC viability was positively correlated with calcium deposition. These findings suggest that titanium surface morphology may modulate mineralization-associated responses in GMSCs.