In order to evaluate whether nonsurgical periodontal treatment with/without diode laser (DL) decontamination improves clinical parameters, the levels of IL-1β, IL-6, IL-8, intercellular adhesion molecule (ICAM), and vascular cell adhesion molecule (VCAM) in gingival crevicular fluid and metabolic control (HbA1c) in chronic periodontitis (CP) patients with diabetes mellitus type 2 (DM2). Sixty patients with DM2 and CP were randomly assigned into two groups to receive scaling and root planing (SRP, n = 30) or SRP followed by diode laser application (SRP + DL, n = 30). Clinical periodontal and gingival crevicular fluid (GCF) parameters were assessed at baseline, 1, and 3 months after periodontal treatment. HbA1c levels were evaluated at baseline and 3 months post-therapy. Total amounts of cytokines and molecules were analyzed by ELISA. Nonsurgical periodontal treatment with/without DL appeared to improve clinical, biochemical parameters, and glycemic control in DM2 patients (BMI < 25 kg/m2) with CP. The SRP + DL group provided better reductions in probing depth (PD) and clinical attachment level (CAL) parameters compared to the SRP group (P < 0.05). Significant reductions were found in the total amounts of GCF levels of IL-1, IL-6, IL-8, ICAM, and VCAM after treatment (P < 0.05). HbA1c levels decreased significantly at 3 months after treatment (P < 0.05). SRP + DL reduced HbA1c levels more significantly compared to SRP alone (0.41 vs. 0.22 %, P < 0.05). SRP, especially in combination with DL, shows improvement of glycemic control for DM2 patients with CP.