Atmospheric ammonia is an important air pollutant, while dairy production is a significant source of ammonia emissions. The aim of the present dairy manure management study was to analyze: 1) the impacts of acidification of the manure surface and/or a vermiculite cover on ammonia, nitrous oxide and methane emissions from animal housing and manure storage stages, 2) the potential influence on the reactive nitrogen (N) and carbon (C) footprints of milk from cradle-to-farm-gate. It was based on a consecutive incubation trial and a life cycle assessment approach for a typical dairy farm system on the North China Plain. Trial results showed that surface-acidification of manure under a slatted floor could reduce ammonia emission by 98 and 22% from housing (one day) and storage stages (38 days), respectively, with small effects on nitrous oxide and methane emissions. The vermiculite cover (storage stage only) reduced ammonia emissions by 98% and methane by 58%, but increased nitrous oxide emissions from storage by almost six times with small absolute losses. The combination of the two mitigations retained 90% of the manure N post-storage relative to that at the start of the housing stage. Life cycle assessment indicated that the reactive-N footprint (NF, i.e. reactive N loss per kg fat- and protein-corrected milk) of milk production was dominated by ammonia emissions and was reduced by 10, 33 and 38% in the manure acidification, manure cover and combination treatments, respectively. Acidification of the manure surface, the vermiculite cover and combination treatments decreased the C footprint (CF, i.e. total greenhouse gas emissions per kg fat- and protein-corrected milk) by 1.0, 1.9 and 2.4%, respectively. This holistic analysis, combining incubation trials and life cycle assessment, indicates that surface-acidification of manure under the slatted floor and a vermiculite cover during manure storage can reduce ammonia emission from a dairy farm system, with an overall positive influence on reduction of NF and CF for dairy farm systems. (C) 2020 Elsevier Ltd. All rights reserved.