School lunch programs provide an opportunity to improve students’ diets. We sought to determine the impact of a multifaceted intervention (cafeteria redesigns, increased points-of-sale and teacher education) on secondary students’ perceptions of school-lunch quality and convenience and fruit and vegetable intake. Surveys ( n = 12,827) from middle and high school students in 12 intervention and 11 control schools were analyzed. We investigated change in school-lunch perceptions and lunchtime and daily fruit and vegetable consumption from 2016 to 2018. Among 8th graders, perceptions that school lunch tastes good and that school lunch was enough to make students feel full increased 0.2 points (on a 5-point scale; p < 0.01) in intervention schools relative to control schools. Among 10th graders, lunchtime fruit and vegetable consumption increased 6% in intervention relative to control schools ( p < 0.05 and p < 0.01 respectively). Daily fruit intake increased 0.1 cups/day in intervention relative to control schools among 9th graders ( p < 0.01). This study provides important evidence on the limited effect of design approaches in the absence of meal changes. We observed only modest changes in school lunch perceptions and fruit and vegetable consumption that were not consistent across grades, suggesting that additional efforts are needed to improve school-lunch uptake.