Several physical and physiological indices have been used to assess white-tailed deer (Odocoileus virginianus) nutritional condition and habitat quality. We tested whether indices reflected inferred nutritional circumstances under controlled conditions of dietary protein and energy at 2 time scales. Our study used adult female deer that were captured in southern Texas and placed in captivity. We randomly assigned deer (n = 51) in the long-term study to 4 diet groups representing a factorial combination of 2 levels each of crude protein (CP) and energy for 6 months. We assigned deer (n = 31) in the short-term study to 6 diets (a factorial combination of 3 levels of CP and 2 levels of energy) for 60 days. At the end of the experimental periods, we sacrificed deer and assessed their nutritional status from serum (n = 11), ruminal (n = 3), fecal (n = 4), fat (n = 7), and carcass (n = 7) indices. Protein-energy interaction effects (P < 0.05) were observed for serum (calcium [Ca], phosphorus [P]), ruminal (neutral detergent fiber [NDF]), and fecal (NDF, dry matter) indices in both experiments. Six-month trials also had protein-energy interactions (P < 0.05) for serum (urea nitrogen, creatinine), ruminal digestible energy (DE), and fecal nitrogen. Sixty-day trials had protein-energy interactions (P < 0.05) for serum alkaline phosphatase, kidney mass (KM), relative KM, back fat depth, and eviscerated body mass (EBM). Nutritional indices in all categories (e.g., fecal, ruminal, carcass) varied (P < 0.05) by dietary protein status, dietary energy status, or protein-energy interactions. Multiple indices are recommended to assess deer herd condition and habitat quality. However, because multiple indices may not be available because of limited availability and resources, we provided variables in each index category that discriminate among nutritional levels.