Providing flavored milk in school lunches is controversial, with conflicting evidence on its impact on nutritional intake versus added sugar consumption and excess weight gain. Nonindustry-sponsored studies using individual-level analyses are needed. Therefore, we conducted this mixed-methods study of flavored milk removal at a rural primary school between May and June 2012. We measured beverage selection/consumption pre- and post-chocolate milk removal and collected observation field notes. We used linear and logistic mixed models to assess beverage waste and identified themes in staff and student reactions. Our analysis of data from 315 unique students and 1,820 beverages choices indicated that average added sugar intake decreased by 2.8 g postremoval, while average reductions in calcium and protein consumption were negligible (12.2 mg and 0.3 g, respectively). Five thematic findings emerged, including concerns expressed by adult staff about student rebellion following removal, which did not come to fruition. Removing flavored milk from school-provided lunches may lower students' daily added sugar consumption without considerably decreasing calcium and protein intake and may promote healthy weight.