This case report presents a 3-year follow-up of the clinical outcomes of a combined surgical therapy for advanced peri-implantitis with concomitant soft tissue volume augmentation using a collagen matrix. One patient suffering from advanced peri-implantitis and a thin mucosal biotype underwent access flap surgery, implantoplasty at buccally and supracrestally exposed implant parts, and augmentation of the intrabony components using a natural bone mineral and a native collagen membrane after surface decontamination. A collagen matrix was applied to the wound area to increase soft tissue volume and support transmucosal healing. The following clinical parameters were recorded over a period of 3 years: bleeding on probing (BOP), probing depth (PD), mucosal recession (MR), clinical attachment level (CAL), and width of keratinized mucosa (KM). At 36 months, the combined surgical procedure was associated with a clinically important reduction in mean BOP (100%), PD (4.3 ± 0.5 mm), and CAL (4.4 ± 0.4 mm). Site-level analysis of the buccal aspects pointed to an increase in MR (-1.0 ± 0.4 mm) and a decrease in KM (-1.3 ± 0.5 mm) values at 12 months. However, a regain in mucosal height and KM was noted at 24 months, even reaching respective baseline values after 36 months of healing. The presented combined surgical procedure was effective in controlling an advanced peri-implantitis lesion without compromising the overall esthetic outcome in the long term.