Fish regulate nutrient intake and allocation to satisfy nutritional and energetic demands, creating trade-offs among maintenance, growth, and waste production. While these processes are well studied in aquaculture, insights from nutritional physiology and environmental impacts are often considered in isolation. Organism-demand-based frameworks offer a means to integrate these perspectives but remain underutilised in aquaculture. This is particularly important as consideration of aquaculture feeds to help achieve wider sustainability objectives must better meet requirements for higher growth performance and lower environmental impact. Here, we apply the organism-demand-based geometric stoichiometry framework to Atlantic salmon (Salmo salar) and calibrate it using experimental data from feeds containing different protein sources to quantify how absorbed nutrients are allocated across physiological processes and associated trade-offs. Feed composition altered nutrient allocation patterns and elemental budgets across the different treatments. All feeds were lipid-limited to varying degrees, with lower lipid availability increasing protein catabolism and nitrogen excretion, thereby reducing protein allocation to growth. Respiration dominated carbon losses across all feeds, whereas nitrogen loss occurred primarily through metabolic excretion and varied significantly among treatments. Sensitivity analyses highlighted the importance of protein allocation and synthesis efficiency in shaping predicted waste outputs. Relative to the experiment and geometric stoichiometry model, the conventional bioenergetic model systematically overestimated growth and underestimated faecal C:N ratios, reflecting differences in nutrient accounting and representation of physiological processes, rather than feed-specific effects. By explicitly linking nutrient demand, physiological trade-offs, and waste production, geometric stoichiometry provides a promising mechanistic framework to help support studies that seek to improve feed efficiency and reduce waste.