Ammonia (NH3) loss following manure application is an environmental concern and N loss for crop production. Manure injection typically reduces NH3 loss compared to surface application without incorporation but increases emissions of nitrous oxide (N2O), which is a potent greenhouse gas. Synchronizing manure in spring with cover crop (CC) growth may increase N recovery and reduce N2O emissions compared to applying manure later in the absence of growing crops. We compared the two following manure application methods: shallow‐disk injection (IM) or surface banding without incorporation (BM) to annual ryegrass (Lolium multiflorum L.) and red clover (Trifolium pratense L.) CC at two times: early spring on growing CC (EARLY) and late spring on terminated CC (LATE). The randomized split‐plot block experiment was conducted at Rock Springs, PA, during 2021–2022. After manure application, we measured NH3 for 72 h and N2O throughout the growing season. Aboveground CC biomass, N, and C:N ratio; pre‐sidedress soil nitrate; corn (Zea mays L.) stalk nitrate; and silage yield were assessed. Averaged across application times, compared to BM, IM reduced cumulative NH3 loss, increased soil N, and resulted in 13% greater corn yield but increased yield‐scaled N2O. Compared to BM LATE, BM EARLY reduced NH3 loss by 43%, increased CC N, reduced N2O emission by 50%, but decreased corn yield by 11%. When IM was EARLY compared to LATE, CC N increased 84%, cumulative N2O loss decreased 55%, and corn yield was similar. Injecting manure to growing CCs offers a strategy for reducing detrimental NH3 and N2O emissions and maintaining corn yield.