This meta-analysis was conducted to investigate the efficacy and safety of antimicrobial photodynamic therapy used alone or adjunctive to scaling root planing in patients with chronic periodontitis. The meta-analysis was conducted according to the QUOROM statement and recommendations of the Cochrane Collaboration. An extensive literature search was performed on seven databases, followed by a manual search. Weighted mean differences and 95% confidence intervals were calculated for clinical attachment level, probing depth and gingival recession. The I(2) test was used for inter-study heterogeneity; visual asymmetry inspection of the funnel plot, Egger's regression test and the trim-and-fill method were used to investigate publication bias. At 3 months, significant differences in clinical attachment level (p = 0.006) and probing depth reduction (p = 0.02) were observed for scaling root planing with antimicrobial photodynamic therapy, while no significant differences were retrieved for antimicrobial photodynamic therapy used alone; at 6 months no significant differences were observed for any investigated outcome. Neither heterogeneity nor publication bias was detected. The use of antimicrobial photodynamic therapy adjunctive to conventional treatment provides short-term benefits, but microbiological outcomes are contradictory. There is no evidence of effectiveness for the use of antimicrobial photodynamic therapy as alternative to scaling root planing. Long-term randomized controlled clinical trials reporting data on microbiological changes and costs are needed to support the long-term efficacy of adjunctive antimicrobial photodynamic therapy and the reliability of antimicrobial photodynamic therapy as alternative treatment to scaling root planing.