This study evaluated the impact of peri-implant treatment in the salivary levels of Colony stimulator factor -1 (CSF-1), S100A8/A9 and S100A12 in patients having mucositis or peri-implantitis. As a secondary aim, we analysed the correlation between the salivary and peri-implant crevicular fluid (PICF) levels. Forty-seven patient, 27 having mucositis (mean age 63.11 ± 7.78) and 20 having peri-implantitis (61.25 ± 7.01) participated in the study. Clinical parameters, probing pocket depth, clinical attachment level, % of plaque and bleeding on probing were evaluated. Unstimulated whole saliva was collected from all patients, while PICF was collected only from a patient’s subgroup (n = 20). Samples were collected before and 3 months after peri-implant treatment. Enzyme-linked immunosorbent assays determined levels of CSF-1, S100A8/A9 and S100A12. Clinical parameters improved and salivary levels of CSF-1 and S100A8/A9, but not S100A12, reduced significantly after treatment in both groups. No significant correlation was found in the salivary and PICF levels of the same molecule. In conclusion, the treatment of peri-implant disease significantly improved the clinical parameters and reduced the salivary levels of CSF-1 and S100A8/A9. The salivary expressions of CSF-1, S100A8/A9 and S100A12 did not correlate with their own expression in PICF.