Crowding is a complex stress that can affect organisms’ physiology, especially through decreased food quality and accessibility. Here, we evaluated the effect of larval density on several biological traits of Drosophila melanogaster. An increasing gradient, from 1 to 1000 eggs per milliliter of food, was used to characterize life-history traits variations. Crowded conditions resulted in striking decreases of fresh mass (up to six-fold) and viability, as well as delayed development. Next, we assessed heat and cold tolerance in L3 larvae reared at three selected larval densities: low (LD, 5 eggs.mL−1), medium (MD, 60 eggs.mL−1) and high (HD, 300 eggs.mL−1). LT50 values of MD and, to a lesser extent, HD larvae were repeatedly higher than those from LD larvae, under both heat and cold stress. We investigated potential physiological correlates associated with this density-dependent thermotolerance shift. No marked pattern could be drawn from the expression of stress-related genes. However, a metabolomic analysis differentiated the metabotypes of the three density levels, with potential candidates associated with this clustering (e.g. glucose 6 phosphate, GABA, sugars and polyols). Under HD, signs of oxidative stress were noted but not confirmed at the transcriptional level. Finally, urea, a common metabolic waste, was found to accumulate substantially in food from MD and HD. When supplemented in food, urea stimulated cold tolerance but reduced heat tolerance in LD larvae. This study highlights that larval crowding is an important environmental parameter that induces drastic consequences on flies’ physiology and can affect thermotolerance in a density specific way.