Background Peri-implant diseases are caused by biofilms around the implant and may lead to implant failure. Non-surgical mechanical debridement (MD) with different adjunctive therapies has been applied in the treatment of peri-implant diseases. This systematic review aimed to deduce the optimal adjunctive therapy. Methods Two independent authors screened the literature using MEDLINE and Cochrane Library. Only clinical randomized controlled trials (RCTs) about adjunctive therapies for non-surgical treatment of peri-implant diseases were included in this review. Studies selected were published before February 2020. The clinical outcomes were compared in this meta-analysis. Results: A total of 31 RCTs met the inclusion criteria. The following adjunctive interventions were compared in the included studies: modification of the prosthesis; air abrasive; Er:YAG laser; diode laser; photodynamic therapy; local antibiotics; system antibiotics; probiotics; and enamel matrix derivative. Follow-up ranged from 3 months to 1 year. A statistically significant difference was observed between MD with photodynamic therapy and MD alone at 3 months follow-up ( P < 0.01). However, such a difference was not detected between MD with chlorhexidine and MD alone at 3 months follow-up ( P = 0.61), between MD with probiotics and MD alone ( P = 0.47), and between systemic antibiotics and MD alone ( P = 0.96). Conclusion Currently, the optimal non-surgical intervention is not known. Also, among the interventions with similar efficiency, that with fewer side effects, easy to use, and cost-effective is yet to be identified. Thus, well-designed RCTs with prolonged follow-ups to assess the accurate effectiveness of therapies are imperative.