Despite the beneficial effects shown when the mitochondrial alternative oxidase AOX from Ciona intestinalis (Tunicata: Ascidiacea) is xenotopically expressed in mammalian and insect models, important detrimental outcomes have also been reported, raising concerns regarding its envisioned deployment as a therapy enzyme for human mitochondrial and related diseases. Because of its non-proton pumping terminal oxidase activity, AOX can bypass the cytochrome c segment of the respiratory chain and alleviate the possible overload of electrons that occurs upon oxidative phosphorylation (OXPHOS) dysfunction, not contributing though to the proton-motive force needed for mitochondrial ATP synthesis. We have shown previously that AOX-expressing flies present a dramatic drop in pupal viability when the larvae are cultured on a low nutrient diet, indicating that AOX interferes with normal developmental metabolism. Here, we applied combined omics analyses to show that the interaction between low nutrient diet and AOX expression causes a general alteration of larval amino acid metabolism and lipid accumulation, which are associated with functional and morphological alterations of the larval digestive tract and with a drastic decrease in larval biomass accumulation. Pupae at the pre-lethality stage present a general downregulation of mitochondrial metabolism and a signature for starvation and deregulated signaling processes. This AOX-induced lethality is partially rescued when the low nutrient diet is supplemented with tryptophan and/or methionine. The developmental dependence on these amino acids, associated with elevated levels of lactate dehydrogenase, lactate, 2-hydroxyglutarate, choline-containing metabolites and breakdown products of membrane phospholipids, indicates that AOX expression promotes tissue proliferation and growth of the Drosophila larvae, but this is ultimately limited by energy dissipation via mitochondrial uncoupling. We speculate that the combination of diet and AOX expression may be used for the metabolic regulation of proliferative tissues, such as tumors.