The aim of this study was to evaluate the effect of an MB experimental formulation (ethanol 20%) in aPDT used as an adjuvant to scaling and root planing (SRP) in the periodontal treatment of diabetic rats. Forty male Wistar rats received streptozotocin-intraperitonial injections to induce diabetes. After 14 days, 5 animals were allocated in the non-ligate group (NLG), and 35 animals received ligature at the first right mandibular molar to induce periodontitis. After 7 days, the ligature was removed and the animals were randomized into 4 groups: LG (without treatment, n = 5), SRPG (SRP, n = 10), aPDTW (SRP+aPDT-MB/water, n = 10), and aPDTEt (SRP + aPDT-MB/water/ethanol/carboxymethylcellulose, n = 10). Animals were euthanized after 7 days. Data of bone loss (BL) area, degree of inflammatory cell response, and collagen fibers percentages were statistically analyzed (p < 0.05). Percentage of animals that presented mild and severe inflammatory infiltrate was 10% and 40% for SRPG, 20% and 30% for aPDTW, and 50% and 0% for aPDTEt, respectively. BL area (mm) was statistically higher in the LG (0.39 ± 0.15) than NLG (0.05 ± 0.02). aPDTEt showed the lowest value of BL (0.08 ± 0.03), followed by aPDTW (0.21 ± 0.15) and SRPG (0.31 ± 0.18). Statistical differences were verified between aPDTEt and SRPG. In relation to the LG, aPDTEt, aPDTW, and SRPG recovered the equivalent 80%, 46%, and 20% of the BL. aPDTEt showed collagen content statistically higher than SRPG and LG, and presented higher mean values than NLG (p > 0.05). Our findings showed aPDTEt presented promising results. aPDT using MB/ethanol can have potential as an adjunctive periodontal treatment in diabetics.