Before recommending a feeding or management strategy for greenhouse gas (GHG) mitigation, it is important to conduct a holistic assessment of all related emissions, including those arising from feed production, digestion of these feeds, managing manure, and other on-farm production processes and inputs. The cumulating and cascading effects of management practices on emissions from agricultural systems can rarely be measured directly, so whole-farm emissions are normally estimated using mathematical models. An example of such a model is Holos, a whole-farm model and software tool developed by Agriculture and Agri-Food Canada to estimate GHG emissions from Canadian farm systems (www.agr.gc.ca/holos-ghg). Using a whole-systems approach, the Holos model, and experimentally measured data, we compared the effects of alfalfa silage-, barley silage-, and corn silage-based diets on GHG estimates in simulated Canadian dairy production systems. Previous studies showed the impact of silage choice on enteric methane production but the impact of diet choice on GHG emissions from the complete farm system had not been explored. Utilizing the functional units of milk, meat, and total energy in food products generated by the system, the comparison demonstrated very little difference between alfalfa and corn silage production systems in terms of GHGs. In general, GHG emissions associated with barley silage-based diets were higher than those for corn silage-based diets. This demonstrates that reported GHG reduction factors cannot be simply combined additively because the interwoven effects of management choices cascade through the entire farm system, sometimes with counter-intuitive outcomes. Whole-farm analysis of GHG emissions from dairy production and exploration of mitigation strategies is facilitated by the Holos software tool.