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Background: Given the current worldwide epidemic of obesity, there is a demand for interventions with higher impact, such as those carried out in the primary health care (PHC) setting. Here we evaluate the effect of intervention performed according to the stages of change of the transtheoretical model (TTM) for weight management. Methods: This randomized controlled trial in Brazilian PHC offered free physical exercise and nutrition education. The participants were women, aged 20 years or older who were obese or overweight, users in PHC service. The intervention group (IG, n = 51) received the same orientation as the comparison group (CG, n = 35) plus individual health counseling based on the TTM aimed at weight loss, which lasted 6 months. The outcome measures were anthropometric, food, and nutrient profiles. Inflammatory parameters were evaluated in a random subsample. The inter-group and intra-group differences were evaluated using interntion-to-treat analysis, and analysis of covariance (ANCOVA) used to assess intervention effectiveness. Results: There was a difference between groups of − 1.4 kg (CI95%: − 2.5; − 0.3) in body weight after the intervention. About 97% of women in the IG reported benefits of the intervention and presented positive changes in diet, biochemical markers, and anthropometry. The IG showed better body mass index, resistine, and blood glucose results compared to the CG during follow-up. Conclusion: The individualized TTM-based intervention, combined with usual care, was an effective strategy in PHC. These results should encourage the use of interdisciplinary practices; nevertheless, research to identify additional strategies is needed to address barriers to weight maintenance among obese low-income women. Trial registration: The trial is registered with Brazilian clinical trials under the code: RBR-8t7ssv, Registration date: 12/12/2017 (retrospectively registered).