Background/Objectives: Cytokines related to the Th17 response have been associated with peri-implant diseases; however, the effect of peri-implant therapy on their modulation remains underexplored. To evaluate the effect of peri-implant therapy on the expression of cytokines related to the Th17 response in the peri-implant crevicular fluid (PICF) (GM-CSF, IFN-γ, IL-1β, IL-4, IL-6, IL-10, IL-12 (p70), IL-17A, IL-21, IL-23, and TNF-α) of partially edentulous patients with peri-implant disease (PID). Methods: Thirty-seven systemically healthy individuals presenting with peri-implant mucositis (PIM) (n = 20) or peri-implantitis (PI) (n = 17) were treated and evaluated at baseline (T0) and three months after therapy (T1). Clinical parameters (probing depth (PD), clinical attachment level (CAL), plaque index, and bleeding on probing index (BoP), were evaluated. The PIM group underwent non-surgical therapy, while the PI group received a surgical approach. PICF was collected with absorbent paper strips and analyzed with a multiplex assay. Results: Eighty-eight implants were treated in 37 patients (56 in the PIM group and 32 in the PI group). After therapy, significant reductions in PD, CAL, plaque index, and BoP were observed in the PIM group (p < 0.05). In the PI group, significant reductions in PD, CAL, and BoP were noted (p < 0.05). The PIM group showed a significant reduction of IL-17A and TNF-α after therapy, while the PI group showed a significant reduction of IL-1β, IL-6, and TNF-α (p < 0.05). Conclusions: The peri-implant therapy for patients with PID reduced the expression of cytokines related to the Th17 response in PICF.