Abstract Background In 2016, Chile implemented the Food Labeling and Advertising Law to fight childhood obesity through front-of-package food labelling, marketing restrictions and school activities and programs. Nevertheless, little is known on its influence on key stakeholders in vulnerable peripheral regions of the country. This study aimed at identifying important influencing factors including the Food Labeling and Advertising Law on dietary habits and physical activity patterns of second graders in Chile, as perceived by school representatives and the children themselves. Methods Semi-structured interviews with four school directors and 17 groups of three second graders, informal interviews with 9 key teachers and 4 food services staff complemented with documented observations were carried out in four primary schools of the Chilean city of Punta Arenas, in the Magallanes Punta Arenas region. The different sources allowed for triangulation of results. Results FLAL seems to have a negligible influence on young children’s diet and physical activity in the study region. Barriers are children’s deeply rooted dietary habits, excessive screen-time, the parents’ lacking problem awareness, limited time for parenting practices and bad role modeling. Environmental barriers are overloaded schools due to insufficient coordination between governmental entities, lacking funds for sound teacher training and unsafe neighborhoods limiting children’s play. Conclusions Policy interventions aimed at reducing childhood obesity need to include and empower schools, families and local communities as active partners and consider their framework conditions for greater influence on dietary habits and physical activity.