Background <p>Since 2020, New Zealand’s free, healthy lunch program, Ka Ora, Ka Ako, has been implemented in qualifying schools from high-deprivation areas. The aim of this study was to measure its impact on student health and wellbeing.</p> Methods <p>A quasi-experimental study compared health and wellbeing outcomes for Year 5 and Year 9 students in Hawke’s Bay in participating versus non-participating schools using surveys of eating behaviours, food insecurity, wellbeing (WHO-5 questionnaire), and body size (anthropometry) in 2020 and 2023.</p> Results <p>Compared to students from 14 non-Ka Ora, Ka Ako schools (<i>n</i> = 741/690), students from 13 Ka Ora, Ka Ako schools (<i>n</i> = 447/399 2020/2023) had: generally lower vegetable and fruit consumption at baseline, but non-significant increases in any vegetables (<i>p</i> = 0.149) and any fruit (<i>p</i> = 0.09) over time; higher unhealthy food consumption at baseline which significantly improved over time (<i>p</i> = 0.04); higher food insecurity with no significant change over time; no difference at baseline or change in quality of life scores; substantially higher overweight/obesity prevalence at baseline (66.7% versus 38.0%), and no changes over time (62.0% versus 37.4% at follow up, <i>p</i> = 0.157).</p> Conclusions <p>Ka Ora, Ka Ako has resulted in improvements in eating patterns, but longer duration is needed to determine the impact on overweight/obesity.</p>