Health promotion from an early age is key to preventing unhealthy weight development in childhood, and parental involvement is essential. The school-based Healthy School Start intervention aims to promote healthy dietary and activity habits in the home environment and prevent child obesity through parental support. This study evaluated the effectiveness of the third iteration of the programme on children's dietary and activity behaviours, and body composition through a cluster-randomised controlled trial. The trial included 17 schools (8 intervention) in disadvantaged areas in mid-Sweden with 353 families with 5- to 7-year-old children. The primary outcomes were intake of selected healthy and unhealthy foods and beverages measured using photography. Secondary outcomes were physical activity and sedentary time measured by accelerometry, and measured weight and height. All outcomes were assessed at baseline and post-intervention (8 months). Linear multi-level regression showed significant favourable effects of the intervention for intake of sweet beverages (b = - 0.17, p = 0.04), intake of healthy foods (b = 0.11, p = 0.04), and more time in moderate to vigorous physical activity during weekdays (b = 5.68, p = 0.02). An unfavourable sub-group effect of the intervention was found for children from families with low education regarding sedentary time on weekends (b = 23.04, p = 0.05). The results align with the previous two trials of the programme, indicating that school-based parental support is a useful approach for health promotion in young children in disadvantaged areas.