Small grain cover crops increase surface cover, anchor residues, increase infiltration, reduce erosion, scavenge excess nutrients from the soil, and are easily obtained and inexpensive compared to other cover crop options. The use of small grain cover crops in fields where manure application occurs should increase nitrogen (N) recovery and cycling for use in subsequent crops. The objectives of this study were to determine if a rye (Secale cereale L.) cover crop increases N retention after soil application of swine lagoon slurry and reduces gaseous N losses. Experiments were conducted in a controlled environment chamber using plastic buckets as the experimental units. Three manure-N loading rates were used (0, low, high) and nitrate leaching and N₂O and NH₃ emissions were measured. Cumulative nitrate load in the drainage water was less than 3.1 kg ha^-1 NO₃-N for rye treatments regardless of the manure treatment. Conversely, the no rye high manure rate treatment lost the most N, 62.8 and 37.7 kg ha^-1 NO₃-N, for experiments 1 and 2, respectively. Manure treatments increased rye shoot dry matter, shoot N concentration, and total shoot N content. Nitrogen uptake by rye accounted for more than 70% of the N lost by the treatments without rye. Rye had lower cumulative N₂O emission than the no rye treatment for the high manure treatment. Rye, however, did not have a significant influence on cumulative N₂O flux for the low manure or the no manure treatments compared to the no rye treatments. Ammonia emissions were low for all treatments during both experiments, which was probably related to the rapid manure incorporation after application. Rye can increase N retention and reduce cumulative N₂O emissions and cumulative N load in drainage water when manure is applied to soils.