Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem-effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwa- ter fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichio- metric composition of bodies and excretion) of threespine stickleback. We use two populations from distinct freshwater lineages with contrasting lateral plating pheno- types (full vs. low plating) and their hybrids, which are mostly fully plated. We found that ontogeny, rearing environment, and body condition were the most important pre- dictors of organismal stoichiometry. Although elemental composition was similar be- tween both populations and their hybrids, we found significant divergence in phosphorus allocation among body parts and in phosphorus excretion rates. Overall, body armor differences did not explain variation in whole body phosphorus, phospho- rus allocation, or phosphorus excretion. Evolutionary divergence between these line- ages in both allocation and excretion is likely to have important direct consequences for ecosystems, but may be mediated by evolution of multiple morphological or physi- ological traits beyond plating phenotype.