Aim To examine the adjunctive effect of a Lactobacillus reuteri probiotic (ATCC PTA 5289 & DSM 17938) on the re‐instrumentation of residual pockets. Materials and Methods This randomized, double‐blind, placebo‐controlled study included 39 previously non‐surgically treated periodontitis patients. A re‐instrumentation was carried out, and probiotic and/or placebo drops were applied according to the study protocoll. Patients afterwards received lozenges to use 2×/day for 12 weeks. Probing pocket depth (PPD), recession, bleeding on probing and plaque levels were analysed, next to the microbiological impact. Results No effects of the probiotic drops could be found. However, after 24 weeks, the overall PPD in the probiotic lozenges group (2.64 ± 0.33 mm) was significantly lower compared to the control lozenges (2.92 ± 0.42 mm). This difference was even more pronounced in moderate (4–6 mm) and deep (≥7 mm) pockets. In the probiotic lozenges group, there were also significantly more pockets converting from ≥4 mm at baseline to ≤3 mm at 24 weeks (67 ± 18% versus 54 ± 17%) and less sites in need for surgery (4 ± 4% versus 8 ± 6%). However, the probiotic products did not influence the microbiological counts of the periodontopathogens. Conclusion The adjunctive consumption of L. reuteri lozenges after re‐instrumentation improved the PPD reduction, without an impact on pocket colonization with periodontopathogens.