Summary Background and Objective The aim was assessing a short training for healthcare providers on patient‐focused counselling to treat childhood obesity in primary care, along with dietitian‐led workshops and educational materials. Methods Randomized clustered trial conducted with paediatrician‐nurse pairs (Basic Care Units BCU) in primary care centres from Tarragona (Spain). BCUs were randomized to intervention (MI) (motivational interview, dietitian‐led education, and educational materials) or control group (SC, standard care). Participants were 8–14‐year‐old children with obesity, undergoing 1–11 monthly treatment visits during 1 year at primary care centres. The primary outcome was BMI z‐score reduction. Results The study included 44 clusters (23 MI). Out of 303 allocated children, 201 (n = 106 MI) completed baseline, final visits, and at least one treatment visit and were included in the analysis. BMI z‐score reduction was −0.27 (±0.31) in SC, versus −0.36 (±0.35) in MI (p = 0.036). Mixed models with centres as random effects showed greater reductions in BMI in MI than SC; differences were B = −0.11 (95% CI: −0.20, −0.01, p = 0.025) for BMI z‐score, and B = −2.06 (95% CI: −3.89, −0.23, p = 0.028) for BMI %. No severe adverse events related to the study were notified. Conclusion Training primary care professionals on motivational interviewing supported by dietitians and educational materials, enhanced the efficacy of childhood obesity therapy.