Background This study explored the effects of Project Daire, a school-based food intervention, on secondary dietary outcomes Diet Diversity Score (DDS) and Diet Quality Score (DQS), among 6–7 and 10-11-year-old children. Methods A randomised-controlled, factorial design trial was conducted in 15 Northern Ireland primary schools across four intervention arms: Nourish, Engage, Nourish and Engage, and Control (Delayed). Nourish modified the school food environment and increased exposure to local foods, while Engage delivered educational activities on nutrition, food, and agriculture. Food consumption data were collected at baseline and at up to a 6-month follow-up. DDS and DQS (at home, at school and/or total) were determined based on the UK Eatwell Guide. Results A total of 445 children aged 6–7 and 458 aged 10–11 completed the trial. Among the 10-11-year-olds who received the Nourish intervention, significant increases were observed in the school DDS (adjusted mean difference = 2.79, 95% CI: 1.44–4.14; p < 0.001) and total DDS (adjusted mean difference = 1.55, 95% CI: 0.65–2.44; p = 0.001) compared to their counterparts who did not receive it. No such changes were observed in the DDS of 6-7-year-olds in the Nourish group, nor in either age group receiving the Engage intervention. The DQS of both age groups remained unchanged across all intervention groups. Conclusions The Nourish intervention was associated with improved dietary diversity among older children through modifications to the whole-school environment. However, the absence of measurable effects on diet quality highlights the need for future iterations of Project Daire to incorporate additional strategies. These should include targeted approaches to improve diet quality, foster active parental engagement, utilize validated dietary assessment tools, and ensure sustained implementation.