Background <p>Multimorbidity is defined as the presence of two or more multifactorial diseases or conditions. In this context, the focus of this study is on arterial hypertension (AH) and diabetes, two chronic diseases with high global prevalence and incidence, whose clinical, physical, and behavioral factors must be critically analyzed over the long term, particularly within the primary care setting, where interventions are most effective and impactful. The objective of the study was to prospectively assess baseline levels of clinical, physical, and behavioral parameters and their changes over three years in adults and older adults with AH and/or diabetes receiving primary care.</p> Methods <p>A three-year prospective cohort study involving 357 individuals previously diagnosed with AH and/or diabetes. These individuals received an intervention based on general guidance regarding health care, healthy choices, and positive behavioral changes. This intervention took place at the beginning of the study (T0 – baseline) and at the end of the study (T1 – follow-up), and the patients were divided as follows: Group 1 (diabetes diagnosis only); Group 2 (AH only); and Group 3 (diabetes and AH). Changes in physical, clinical, anthropometric, and behavioral parameters among the groups were statistically analyzed between T0 and T1 using the Kruskal–Wallis H test and the chi-square test. Additionally, post hoc multiple comparisons were performed using Tukey’s test and Dunn’s test with Bonferroni adjustment. Effect sizes were estimated using Cohen’s d with corresponding 95% confidence intervals.</p> Results <p>Within-group comparisons revealed a significant reduction in physical activity levels in Group 2, while Group 3 showed improvements in HbA1c (d = − 0.40; <i>p</i> = 0.034), SBP (<i>p</i> = 0.025), DBP (<i>p</i> = 0.003), and BMI (<i>p</i> = 0.003). Between-group comparisons at T1 indicated moderate to large differences in triglycerides (d = 0.53; <i>p</i> = 0.009), which increased over the follow-up period and a significant difference in light physical activity (d = 0.35; <i>p</i> = 0.043).</p> Conclusions <p>The results indicate that lifestyle improvements in patients diagnosed with hypertension and/or diabetes are associated with improvements in cardiometabolic indicators. Although group interventions are important, individualized approaches tend to promote better adherence and self-care, demonstrating that chronic disease management strategies in primary care can help reduce the burden on health care services.</p> Trial registration <p>Brazilian Registry of Clinical Trials (ReBEC), ID: RBR-45hqzmf.</p>