Background: Schools are a promising site for influencing the dietary intake of children and adolescents. The US Department of Agriculture recently released flexibilities to requirements for whole-grains, sodium, and low-fat milk in schools who demonstrated difficulty meeting nutrition standards for school meal programs. The support of School Nutrition Directors (SNDs) is vital to the success of school food environment changes; however, few studies have explored SNDs perceptions to changes in nutrition standards. Methods: Experiences and perspectives toward nutrition standards of 10 SNDs, and their satisfaction with flexibilities for whole-grains, sodium, and low-fat milk were explored using a semi-structured interview. Responses were analyzed using an inductive approach with thematic analysis. Results: Three broad categories emerged challenges with the Healthy, Hunger-Free Kids Act, food preferences and acceptability, and support and representation. A greater need for internal and external support, assistance in equipment and staff, procurement of foods compliant with regulations and acceptable to students, and more input on federal decisions and policies were perceived as important. Conclusions: Results provide critical insight into the implementation of nutrition standards. Future research and changes to school nutrition programs should consider these challenges as they strive to meet the needs of this important population.