Introduction: Epidemiological investigations on tuberculosis-diabetes comorbidity using spatial analysis should be encouraged towards a more comprehensive view of the health of individuals affected by such comorbidity in different contexts. This study analyzes the territories vulnerable to tuberculosis-diabetes comorbidity in a municipality in northeastern Brazil using spatial analysis techniques. Methods: An ecological study was carried out in Imperatriz, Maranhão, Brazil. Tuberculosis-diabetes cases reported in the Brazilian Notifiable Diseases Information System between 2009 and 2018 were analyzed. Kernel density estimation and spatial scanning techniques were used to identify the areas with the greatest occurrence of spatial clusters. Results: A heterogeneous spatial distribution was found, ranging from 0.00 to 4.12 cases/km2. The spatial scanning analysis revealed three high-risk spatial clusters with statistical significance (p < 0.05), involving eleven strictly urban sectors with a relative risk of 4.00 (95% CI: 2.60–6.80), 5.10 (95% CI: 2.75–7.30), and 6.10 (95% CI: 3.21–8.92), indicating that the population living in these areas had a high risk of tuberculosis-diabetes comorbidity. Conclusions: The highest concentration of cases/km2, as well as risk clusters, were found in areas with high circulation of people and socio-economic and environmental vulnerabilities. Such findings reinforce the need for public health interventions to reduce social inequalities.