Method of N application in winter wheat (Triticum aestivum L.) and its impact on estimated plant N loss has not been extensively evaluated. The effects of the pre‐plant N application method, topdress N application method, and their interactions on grain yield, grain protein concentration (GPC), nitrogen fertilizer recovery use efficiency (NFUE), and gaseous N loss was investigated. The trials were set up in an incomplete factorial within a randomized complete block design and replicated three times for 5 site‐years. Data collection included normalized difference vegetation index (NDVI), grain yield, and forage and grain N concentration. The NDVI before and after 90 growing degree days (GDD) were correlated with final grain yield, grain N uptake, GPC, and NFUE. At Efaw location, NDVI after 90 GDDs accounted for 58% of variation in grain yield and 51% variation in grain N uptake. However, NDVI was found to be a poor indicator of both GPC and NFUE. Grain yield was not affected by the method and timing of N application at Efaw. Alternatively, at Perkins, topdress applications resulted in higher yields. The GPC and NFUE were improved with the topdress applications. Generally, topdress application enhanced GPC and NFUE without decreasing the final grain yield. The difference method used in calculating gaseous N loss did not always reveal similar results, and estimated plant N loss was variable by site‐year, and depended on daily fluctuations in the environment.