The aim of this study was to assess the effects of repeated applications of antimicrobial photodynamic therapy (aPDT) on the non-surgical periodontal treatment of residual pockets. This work was performed and reported according to the Cochrane and PRISMA recommendations, respectively, and registered at the PROSPERO registry (number CRD42017058403). An extensive search of the biomedical literature was conducted on four databases from January 1960 to August 2018, followed by hand searching. Analysis of the quality of the selected studies was based on the risk of bias. Only two randomised controlled clinical trials (RCTs) met the inclusion criteria although they had unclear risk of bias. One study showed that repeated applications of aPDT in association with conventional non-surgical treatment during periodontal maintenance improved all clinical outcomes after 6months. The other study, which assessed the effects of repeated applications of aPDT in association with ultrasound debridement on periodontal pathogens, showed no significant reduction of the main pathogens after 3-6months but reported reductions of probing pocket depth and C-reactive protein after 3 and 6months, respectively, compared to mechanical therapy alone. Concluding, it was not possible to state that repeated applications of aPDT, in association with non-surgical treatment of residual pockets, have effective clinical effects in the periodontal maintenance therapy. Although one can consider that aPDT is a promising adjuvant therapy, it is still necessary to carry out more RCTs with low risk of bias in order to confirm or refute the benefits of multiple applications for residual periodontal pockets.