Abstract Background Constipation and obesity have common risk factors. However, little is known about the occurrence of constipation in individuals with severe obesity and the associated factors. Objective To evaluate the prevalence of intestinal constipation and its associated factors in adults with obesity class II and III. Method This study analyzed baseline data from a randomized clinical trial with adults aged 18–64 with a Body Mass Index (BMI) ≥ 35 kg/m², living in the metropolitan region of Goiânia, Brazil. Data were collected using a questionnaire containing sociodemographic, lifestyle, level of obesity, presence of comorbidities, water intake and food consumption variables. The outcome variable was constipation assessed by the Rome III criteria and the Bristol Stool Form Scale. Multiple Poisson regression analysis was used to assess the association between explanatory variables and the outcome. Results Among the 150 participants, the prevalence of constipation was 24.67% (95% CI: 17.69–31.64). After multiple regression analyses constipation was associated with polypharmacy (adjusted PR: 2.99, 95% CI: 1.18–7.57, p = 0.021), younger age group i.e. 18–29 years (adjusted PR: 3.12, 95% CI: 1.21–8.06, p = 0.019) and former smoking (adjusted PR: 3.24, 95% CI: 1.28–9.14, p = 0.014). There was no statistically significant association between constipation and daily consumption of fiber-rich foods, however, the non-consumption of whole grains was borderline significant (adjusted PR: 2.92, 95% CI: 1.00 to 8.49, p = 0.050). Conclusion A high prevalence of constipation was found in adults with obesity class II and III. Constipation was significantly associated with the simultaneous use of five or more medications, younger age group and being a former smoker.