The combined application of manure/slurry and synthetic fertilizer (SF) might be a solution to decrease transport and application costs involving those by-products as well as enable access to them in regions where availability is low. Moreover, their joint application can potentially reduce environmental pollution, enlarge the manure benefits to more areas, and enhance the SF efficiency. However, such a strategy might result in increased ammonia emissions when applied to crop residues. Two experiments were implemented to assess ammonia emissions from stubble-covered soil fertilized with manure amended with SF. In Experiment 1 (E1), urea (U) and calcium ammonium nitrate (AN) were applied combined with dairy manure (MAN). In Experiment 2 (E2), urea was combined with acidified pig slurry (APS) and applied just after sowing (T0) or eight days later (T8). The combinations U + MAN and AN + MAN increased the ammonia emissions, while APS decreased the emissions from U, in APS + U combination, by more than 75%. Therefore, manure combined with SF applied on stubble-covered soil should not be recommended. T8 reduced ammonia emissions from U. APS enhanced the efficiency of U, being then an interesting strategy to mitigate ammonia emissions when applied on stubble-covered soil, as in no-tillage.