Mitochondrial function relies on close coordination between the mitochondrial and nuclear genomes. Disruption to this coordination—via mitonuclear mismatch—can impair metabolic efficiency, particularly under energetically demanding conditions such as during development. The nutritional environment further modulates mitochondrial demands, suggesting that mitonuclear genotype and diet may interact to shape life-history traits and behaviour. Here, we investigate how early-life diet and mitonuclear genotype jointly influence development time, adult body size, and nutritional preference in Drosophila melanogaster. Using a full-factorial panel of putatively matched and mismatched combinations (cybrids) of mitonuclear genotype derived from natural Australian populations, we reared flies on diets varying in their ratio of macronutrients and assessed how this influenced larval development and subsequent adult diet preference. Developmental rate was significantly influenced by mitonuclear coevolution and diet, with cybrids showing delayed development under all conditions, with dietary extremes exacerbating this effect. Despite this, egg-to-adult viability remained unaffected. Adult nutritional behaviour exhibited clear genotype- and diet-dependent effects. Flies reared on high-protein diets increased carbohydrate intake as adults, while those reared on high-carbohydrate diets increased protein intake, suggesting compensatory feeding responses. Mitonuclear mismatch further modulated nutrient consumption, particularly in females, whose carbohydrate intake was influenced by intergenomic compatibility and early-life dietary conditions. Males’ protein consumption was also impacted by mitonuclear coevolution across all developmental diets. Finally, body size was also shaped by interactions between mitonuclear genotype and diet. Together, our findings demonstrate that mitonuclear compatibility and the composition of the early nutritional environment interact to shape developmental and behavioural phenotypes. These results support a role for mitonuclear coadaptation in mediating metabolic plasticity, highlighting the evolutionary and physiological significance of genotype-specific mitonuclear coordination.