Eradication or suppression of pathogens is a major goal in periodontal therapy. Due to the increase in antibiotic resistance, the need of new disinfection therapies is raising. Photodynamic therapy (PDT) has demonstrated anti-infective potential. No data are available on the use of light-emitting diode (LED) lights as the light source in PDT. The aim of this study was to investigate the microbiological and clinical adjunctive outcome of a new photodynamic LED device, compared to scaling and root planing in periodontitis patients in maintenance [supportive periodontal therapy (SPT)]. In this masked, split-mouth design study, 30 treated chronic periodontitis subjects (mean age, 46.2 years; 13 males) in SPT were included. Two residual interdental sites with probing pocket depth (PPD) ≥ 5 mm in two opposite quadrants, with positive bleeding on probing (BOP) and comparable periodontal breakdown, were selected. PPD, BOP and subgingival microbiological samples for real-time PCR analysis (Carpegen® PerioDiagnostics, Carpegen GmbH, Münster, Germany) were recorded at baseline and 1 week after treatment. Scaling and root planing was performed under local anesthesia. Randomly one of the sites was selected to receive adjunctive photodynamic therapy by inserting a photosensitizer (toluidine blue O solution) and exposing it to a LED light in the red spectrum (Fotosan, CMS Dental, Copenhagen, Denmark), according to the manufacturer's instructions. After 1 week, 73 % of the control sites and 27 % of the test sites were still BOP+. These differences compared to baseline values and in-between groups were statistically significantly different (p < 0.001). Mean PPD decreased from 5.47 mm (±0.68) to 4.73 mm (±0.74, p < 0.001) in control sites and from 5.63 mm (±0.85) to 4.43 mm (±1.25, p < 0.001, test vs control p = 0.01) in the test group. Microbiologically, higher reductions of relative proportions of red complex bacteria were observed in test sites (68.1 vs. 4.1 %; p = 0.01). This study showed that adjunctive photodynamic treatment by LED light may enhance short-term clinical and microbiological outcome in periodontitis subjects in SPT.