Background In a previous pilot study, one‐time application of anti‐Porphyromonas gingivalis gingipain egg yolk immunoglobulin (IgY) into scaling and root planing (SRP)‐treated periodontal pockets showed profound improvement of clinical and bacteriological parameters in patients with chronic periodontitis. The present study aims to evaluate the efficacy of daily use of lozenges fortified with the antibody as an adjunct to non‐surgical therapy in patients with periodontitis. Methods Sixty‐four patients with periodontitis were divided randomly into a test and a placebo group. The groups were treated by SRP followed by a daily use of lozenges containing either specific IgY against P. gingivalis gingipains (test) or a sham‐immune IgY (placebo). Gingival bleeding index (GBI), probing pocket depth (PD) and quantitation of P. gingivalis in the gingival pockets were assessed at baseline and 8 weeks after the initiation of treatment and compared by using Wilcoxon signed rank test, Mann‐Whitney U‐test or t test. Results Both groups showed significant improvement of all parameters at 8 weeks post treatment (P < 0.001). There was a significant difference in reduction of GBI (P < 0.001) and P. gingivalis cell counts (P < 0.05) in the test group compared with the placebo group. The reduction of PD was greater in the test group compared with the placebo group although there was no statistically significant difference between the two groups. Conclusions The adjunctive use of lozenges containing IgY antibody against gingipains from P. gingivalis resulted in clinical and microbiological benefits in the treatment for chronic periodontitis. Additional investigations are needed to examine if the IgY brings benefits to case patients who do not receive SRP.