The association of doxycycline and periodontal treatment in non-controlled diabetes mellitus (DM) has shown positive results on clinical and metabolic parameters. Antimicrobial photodynamic therapy (aPDT) is a local and painless antimicrobial treatment that can be applied in periodontal treatment without systemic risks. The aim of this study was to evaluate the potential improvement of aPDT on clinical and metabolic effects in patients with type 2 diabetes mellitus in conjunction with nonsurgical periodontal treatment plus doxycycline. Thirty patients with type 2 diabetes and diagnosis of chronic periodontitis were treated with scaling and root planning (SRP; N = 15) or SRP plus phenothiazine chloride photosensitizer-induced aPDT (SRP + aPDT, N = 15). Patients of both groups took doxycycline (100 mg/day) for 2 weeks and plaque index, bleeding on probe (BOP), probing pocket depth (PPD), suppuration, clinical attachment level (CAL), and glycated hemoglobin levels (HbA1c) were measured at baseline and 3 months after therapy. An improvement in clinical parameters such as PPD, CAL, S, and BOP between groups was observed but without statistical significance (p > 0.05). Intragroup analysis showed a significant reduction of HbA1c (8.5 ± 0.9 to 7.5 ± 0.1, p < 0.01) in the SRP + aPDT group. The differences of HbA1c between baseline and 3 months were greater for the SRP + aPDT (11.4 %) than SRP (10 %) (0.87 ± 0.9 and 0.4 ± 0.84 respectively; p < 0.05). A single application of the aPDT as an adjunct to periodontal treatment did not show additional benefits in the clinical parameters but resulted in a slight greater decrease in HbA1c.