Poor dietary habits and obesity are more prevalent in lower socio-economic status (SES) communities. The NEAT Girls cluster randomized controlled trial was a school-based obesity prevention program targeting adolescent girls in low SES schools in NSW, Australia. The aim was to evaluate the 12-month impact of key nutrition program messages on dietary intake and food behaviors. Diet was assessed using a validated semi-quantitative food frequency questionnaire (FFQ). Individual foods were categorized into nutrient-dense or energy-dense, nutrient-poor food groups and the percentage contribution to total energy intake calculated. Participants were aged 13.2 ± 0.5 years (n = 330). There were no statistically significant group-by-time effects for dietary intake or food related behaviors, with 12-month trends suggesting more intervention group girls had improved water intakes (59% consuming ≼ three glasses per day to 54% at 12 months vs. 50% to 61% in controls, p = 0.052), with a greater proportion consuming < one sweetened beverage per day (24–41% vs. 34–37% in controls, p = 0.057). Further research including more intensive nutrition intervention strategies are required to evaluate whether dietary intake in adolescent girls attending schools in low SES communities can be optimized.