Next to dry matter (DM) intake, nutritional factors cause considerable variation in methane (CH4) emitted and nitrogen (N) excreted per kg of DM intake or per kg of milk. Rumen function in particular determines CH4 emission and concomitant (amount and site) of N excretion, including the trade-offs between them with changes in nutrition and cow characteristics. Quantification of the interaction between CH4 and N emission hence requires quantification of effects on rumen function in particular. The models available to quantify CH4 emission require the same types of input. The detail of questions posed determines the choice of model and the required level of detail of model inputs needed to investigate mitigation measures and the interaction between CH4 and N emission for a specific farming case. Simulation results with a mechanistic model of enteric fermentation confirmed a profound impact of nutritional measures on both CH4 and N emission, but also demonstrated that nutritional measures to mitigate N excretion can be associated with an increase in CH4 emission. This result demonstrates the need to consider details on the rumen level when the aim is to quantify accurately the net effect on greenhouse gas emission for a specific case studied, which contrasts with applying generic values. As an alternative to models of quantification, on-farm measurement of emission might be pursued by sampling of excreta and air. The principle problem is that concentrations are measured which not necessarily reflect daily rates. Milk production rate is recorded on-farm however, which makes indicators based on milk composition just as promising candidates to estimate CH4 (milk fat) or N (milk urea) emission, provided bias by variation in milk composition unrelated to CH4 and N emission rate can be prevented.