School-based interventions offer a promising setting to promote healthier nutritional behaviours (NB) such as physical activity (PA), sedentary behaviour (SB) and eating behaviour, while addressing weight social inequalities. NB changes may occur before measurable effects on weight, which can take longer to emerge. This study evaluated the overall effectiveness of the school-based Promotion de l’ALIMentation et de l’Activité Physique – INEgalités de Santé (PRALIMAP-INÈS) trial on weight and NB social inequalities reduction among adolescents with overweight or obesity. Adolescents were divided into two intervention groups according to their socio-economic status (socially advantaged and socially less advantaged). NB were self-reported by adolescents. Outcomes were BMI z-score (BMIz), fruit and vegetables (FV) consumption, sweetened products and beverages (SPB) consumption, vigorous/moderate PA, walking and SB. Overall effectiveness was estimated using generalised pairwise comparisons, estimating net benefit for each outcome (δ) and overall net benefit (Δ). Of 985 adolescents (age = 15·3 (sd 0·7 years; 46·7 % boys), those in less advantaged group were 12·5 % more likely to have a favourable change in weight status and NB than those in advantaged group (Δ = 12·5 % (6·1, 19·1 %)). For each outcome, net benefits were as follows: BMIz (δ = 4·2 % (0·0, 8·6)), vigorous PA (δ = 4·2 % (0·4, 8·3)), FV (δ = 3·2 % (0·9, 5·5)), SB (δ = 0·8 % (–1·6, 3·2)), SPB (δ = −0·2 % (–1·1, 0·6)), moderate PA (δ = 0·2 %) (–0·7, 1·1) and walking (δ = 0·2 % (–0·2, 0·6)). Results showed an overall beneficial effect of the PRALIMAP-INÈS trial in reducing social inequalities in weight and NB among adolescents with overweight or obesity. Long-term effectiveness could be expected by reducing social inequalities in NB.