An improved understanding of the potential for dietary protein manipulation to reduce ammonia emissions from dairy farms during various stages of manure handling is needed for both modeling and policy-making efforts. The objective of this study was to assess the effects of dietary protein manipulation on ammonia emissions from relatively freshly voided dairy cow manure in three types of removal systems: scraped manure removal systems, flushed manure removal systems, and flushed manure removal systems with a solids separator. Emissions were measured using a dynamic flux chamber for 12 h or more. Ammonia fluxes and emission factors per mass of manure were not affected by dietary protein content because fluxes depended mainly on total ammoniacal nitrogen (TAN) concentration, which did not vary with diet. However, emissions on a per-cow basis were 12% lower with the diet containing 15.0% crude protein as compared to the one with 17.8% (a change in crude protein of 16%) due to reduced urine output. The largest absolute impact of dietary protein manipulation would be with separated liquids because their emission factor was approximately four times higher than for the other types of manure. While dietary protein manipulation can reduce ammonia emissions from manure during long-term storage, its effectiveness in the hours immediately after manure is excreted is limited because emissions are more sensitive to other factors, including temperature and extent of mixing of the manure, that vary widely under real operating conditions on a farm.