Background: Flaplessly placed one-piece mini dental implants (MDI) are an option to support maxillary overdentures. Evenly distribution of the implants over the atrophic alveolar process implies a risk of accidental sinus perforation in the posterior area which could induce sinus-related pathology. Methods: Thirty-one patients received 5–6 maxillary MDIs. Schneiderian membrane swelling was assessed with CBCT at the deepest point of the sinus in the mid-sagittal plane prior to surgery (baseline), after 2 and 5 years. Additionally, subjective patient-reported rhinosinusitis complaints, the effect of smoking, and gender differences were investigated. Results: Mean thickness of the Schneiderian membrane was 2.87 mm at baseline, 3.15 mm at 2 years, and 4.30 mm at 5 years in 27 of 31 initially treated patients. MDI perforation was detected in 21/54 sinuses. At 2 years, perforation length does not affect membrane thickness whereas baseline swelling does. In smokers, each perforated mm induced 0.87 mm additional swelling. After 5 years, the effect of baseline swelling becomes smaller whereas perforation length became statistically significant, with 0.53 mm increase for every perforated mm. The effect of smoking lost its significance. No relations between gender, membrane thickness changes, or subjective clinical sinus complaints and MDI perforation were found. Conclusion: Accidental MDI sinus perforation induces Schneiderian membrane swelling but does not interfere with clinical sinusal outcome after 5 years.