Background: During periodontal inflammation, bacteria induces chemokine expression and migration of various inflammatory cells. The aim of the study was to learn if periodontal treatment alters salivary concentrations of macrophage activation-related chemokines and if such alterations correlate with abundance of periodontitis-associated bacteria. Methods: Twenty-five patients with periodontitis completed the study (NCT02913248 at clinicaltrials.gov). Periodontal parameters and stimulated saliva samples were obtained at baseline and 2, 6 and 12 weeks after non-surgical periodontal treatment. Salivary concentrations of monocyte chemoattractant proteins (MCP-1-4), macrophage-derived chemokine (MDC), macrophage migration inhibitory factor (MIF), monokine induced by interferon-gamma (MIG), macrophage inflammatory protein (MIP-1α) and interferon-inducible protein (IP-10) were quantified using the Luminex® xMAP™ technique and abundance of bacteria was quantified using next-generation sequencing. Results: The treatment improved all periodontal parameters and caused an increase in the concentrations of MCP-2, MDC and MIP-1α at week 12 compared to baseline, week 2 and week 6, respectively. Salivary concentrations of MCP-1-2, MDC, MIG, MIP-1α and IP-10 correlated with the abundance of specific periodontitis-associated bacteria. Conclusions: Periodontal treatment impacts salivary concentrations of MCP-2, MDC and MIP-1α, which correlate with the abundance of specific periodontitis-associated bacteria. This indicates that these chemokines reflect periodontal status and possess potential in illustrating a response to treatment.