Dairy farmers in the northeast face challenges in the application of manure in fall and on-time planting of cool-season grasses to maximize recovery of residual N and nutrients released from fall applied manure. Ammonia emission from animal manure is a serious environmental concern and can be reduced if cover crop is integrated in the farming system. On-time planting of cover crops can reduce ammonia volatilization from fall, surface-applied manure, and prevents N loss to leaching. A two-year study was conducted in 2015 and 2016 to investigate if time of planting of winter annual rye (Secale cereale L.) along with late fall application of manure when air temperature is low can influence ammonia emission and preserve nitrogen (N) to meet the N requirement of forage rape. Three planting dates (16 September, 30 September, and 14 October) of rye cover crop with two manure application treatments including late-fall application and no manure were assessed for mitigating ammonia volatilization, and also yield and recovery of N by forage rape (Brassica napus L.). The highest rates of ammonia volatilization were detected in the first 24 hours after manure spreading regardless of the treatment. The result indicated that cover crop use significantly limited volatilization compared with no cover crop. The earliest planting date produced 3823 kg ha−1 dry matter of winter rye cover crop that was 16 and 35 percent higher than second and third dates of planting, respectively. The manured cover crop accumulated 132 kg N ha−1 when planted early. However, biomass yield of forage rape was more when planted after all cover crop treatments with manure application. Prior to forage planting, the nitrate-N content in all three soil depths (0–20, 20–40, and 40–60 cm) in the plots with manure was higher than plots with no manure. No significant differences in forage rape yield was detected among winter rye planting dates; however, forage rape planted after winter rye was higher than after no-cover crop. The results of this study suggest that when immediate incorporation of manure into soil is not feasible, establishing cover crop early and then applying manure in the late fall, is a practical management to limit nonpoint source pollution from ammonia loss.