The conservation and management of northern ungulates depends upon our understanding of the influence of habitat associations on the nutritional condition of individuals and population productivity. Adverse foraging conditions in late winter may reduce the availability of body proteins for reproduction. Therefore, assessing nitrogen (N) or protein status in late winter could be a valuable tool to monitor populations of northern ungulates. I collected >1,800 excreta samples to evaluate isotopic metrics of protein status [proportion of serum amino acid N derived from body N (p-AN), proportion of urea N derived from body N (p-UN), and the difference between the isotopic ratios of N (δ¹⁵N) in body tissues and urinary urea (Δ_Body-urea)] in captive and wild populations of muskoxen (Ovibos moschatus) and caribou (Rangifer tarandus) in late winter. I evaluated the dynamics of body protein and δ¹⁵N in a captive population of female muskoxen (2007). Diets and protein status were assessed in populations of wild muskoxen in northern Alaska (2005–2008); a semi-captive (penned) population of wild, pregnant caribou (2006); and wild populations of migratory and sedentary ecotypes of caribou (2006–2008). Captive female muskoxen lost body protein (∼6%) in late gestation and these losses corresponded with the protein deposited in reproductive tissues. The concentration of plasma urea, the p-AN, and p-UN tended to increase throughout winter. During late gestation, most penned pregnant caribou on an ad libitum feeding schedule lost core body mass (55%) and were in negative protein status (54%). For groups of wild muskoxen (n = 30), abundance of preferred forages improved protein status (p-UN; R² = 0.45). At the foraging sites of wild caribou (n = 32), the amount of shrubs in a lichen-rich diet had a positive effect on protein status (Δ_Body-urea, r² = 0.26). Foraging constraints in late winter will decrease the amount of body proteins available for reproduction. However, considerable challenges remain to applying the p-UN as a monitoring tool at broad scales for caribou, but with appropriate consideration, isotopic proxies may be used to evaluate environmental constraints for northern ungulates at small scales.