Surface modification of titanium implants using argon plasma has been shown to enhance their hydrophilicity and cellular adhesion, promoting increased bone deposition on both implant and graft surfaces. Experimental models have demonstrated that, following sinus augmentation, spontaneous sinus mucosa perforations may occur over time near implants and graft particles. The purpose of this study was to assess whether argon plasma treatment of implant surfaces influences bone apposition and the incidence of sinus mucosa perforations. Bilateral sinus lift surgeries were performed in sixteen rabbits. Implants either treated with argon plasma or left untreated (controls) were inserted simultaneously, without graft materials. After 8 weeks, histological examinations were conducted. Collapse of the sinus mucosa occurred at all implant sites. Of thirty-two implants, twenty-four showed mucosal perforations at the apex, and several also presented perforations along the threads. Nearly all implants were surrounded by thinned mucosa (thickness < 40 µm). The apical 2.6–2.9 mm segments lacked osseointegration, with approximately 1.3 mm exposed to the sinus cavity. No statistically meaningful differences were detected between the treated and control implants. Both argon plasma-treated and untreated implants led to mucosal injury and perforation through direct contact. Argon plasma surface modification did not alter the final outcomes.