School Lunch programs are a common strategy to address social inequalities in food access among children, especially food insecurity. The aim of this study was to evaluate the dietary intake and lifestyle habits of children aged 10–12 years enrolled in the School Lunch Program in Greece. A cross-sectional survey of fifth and sixth grade students, School Lunch recipients (n = 609) and control subjects (n = 736), collected data on sociodemographic, nutritional and lifestyle habits via self-reported questionnaires during May–October 2019. Despite enrollment in the School Lunch Program children in this group reported consuming less meals during the day (3.47 ± 1.38 vs. 3.65 ± 1.35, p = 0.002). No differences were seen in intakes of energy and macronutrients, however School Lunch recipients reported lower intakes of cereals/potatoes and legumes but higher fruit intake (2.32 ± 1.59 vs. 1.97 ± 1.72, p < 0.05). School Lunch recipients reported 42min/d and 28min/d higher screen-time during weekdays and weekends, respectively. Linear regression highlighted that dietary quality was not associated with School Lunch enrollment but rather sleep duration and screen time had a stronger influence on dietary habits. Enrollment in a School Lunch Program was linked to sustained differences in sedentary lifestyle habits but less so in dietary habits.