Type 2 diabetes mellitus (T2D) and obesity enhance systemic inflammation, microcirculation and immune disorders, which can make the course of chronic generalized periodontitis more severe. Comparative assessment of clinical and radiological manifestations of the disease in individuals with these conditions is important for interdisciplinary management of patients. The study aimed to conduct comparative assessment of clinical and radiological manifestations of chronic generalized periodontitis (CGP) in obese patients with T2D and those having no somatic disorders. A total of 90 patients with moderate CGP aged 35–60 were assessed, who were stratified into three groups (30 individuals per group) matched for gender and age: without any somatic disorders, with T2D and obesity. OHI-S, SBI, periodontal pocket depth (PPD), сlinical attachment loss (CAL), and radiological signs of bone resorption were assessed; the analysis of correlations with HbA1c, BMI, and lipid profile was conducted. OHI-S was 1.8 ± 0.3 in group I, 2.3 ± 0.4 in group II, and 2.2 ± 0.5 in group III; SBI was 42 ± 9%, 61 ± 11%, and 56 ± 10%, respectively (p < 0.05 for groups II and III compared to group I). PPD and CAL were higher in obese patients with T2D, than in patients having no somatic disorders (p < 0.05), while the differences between groups II and III were non-significant (for PPD p = 0.09). HbA1c levels were correlated to PPD (r = 0.42), CAL (r = 0.39), and SBI (r = 0.36); BMI was correlated to PPD (r = 0.33) and SBI (r = 0.35) (p < 0.05). Thus, T2D and obesity are associated with the more adverse clinical and radiological manifestations of CGP; it is necessary to consider poorer oral hygiene in patients with comorbidities when interpreting intergroup differences.