The aim of this trial was to analyze the effect of implant surface decontamination procedures combined with reconstructive surgical treatment (RST) of peri-implantitis on gene expression levels of selected biomarkers in peri-implant crevicular fluid (PICF). Forty patients diagnosed with peri-implantitis were treated with RST + decontamination of the implant surface using sterile saline and ozone therapy (ozone group) or sterile saline alone (control group). The gene expression levels of interleukin (IL)-6, IL-8, IL-17, vascular endothelial growth factor (VEGF), sclerostin (SOST) and osteoprotegerin (OPG) were evaluated by qPCR analysis at baseline and 6-month follow-up. Changes in cytokine mRNA expression levels were analyzed and compared with clinical/radiographic parameters. Both decontamination methods lead to the downregulations of the selected gene expressions. Ozone group showed significantly higher clinical attachment level (CAL) and radiographic defect fill (DF) values at 6 months compared to the control group (p = 0.026 and p = 0.011). The downregulation of SOST levels was significantly associated with probing depth reduction and radiographic DF (p < 0.05). Implant surface decontamination procedures applied with the RST contribute to a notable reduction in immuno-inflammatory response. The additional use of ozone therapy could have favorable effects in anti-infective regimens of peri-implantitis therapy. SOST, which was found to have significant relationship with both clinical and radiographic outcomes, could be a valuable indicator for the progression of peri-implantitis and may aid the development of new therapeutic strategies for bone gain in the RST of peri-implantitis.