Despite global efforts to promote healthy and sustainable diets, the nutrition transition witnessed among adolescents worldwide poses serious threats to health and environmental sustainability. The present study aimed to assess the change in environmental footprints (EFPs) associated with dietary intakes of adolescents in Lebanon between 1997 and 2009. Data of Lebanese adolescents (10–19 years old) were drawn from national food consumption surveys during two time periods (1997, n = 451; 2009, n = 527). Dietary assessments were conducted using 24-h dietary recalls. EFP metrics, including water, energy and greenhouse gas emissions (GHG), were derived using review of existing life-cycle analyses. All EFPs increased significantly between 1997 and 2009; meat and sugar-sweetened beverages were the top contributors to the increase in these EFPs. The changes in EFPs between the two years remained significant even after adjustment for energy and other correlates: water (β = 267.7, CI: 123.5; 411.9); energy (β = 4.3, CI: 2.09; 6.52) and GHG (β = 0.44, CI: 0.11; 0.76). Findings show significant dietary shifts among adolescents that can threaten the environmental sustainability of Lebanese diets. Interventions across the food system are needed to promote adherence to healthy and sustainable diets among adolescents.