Background: Nitrogen (N) plays an important role within milk production systems (MPS), as an indicator of environmental and economic efficiency. Objective. The objective was to determine utilisation of N offered in the ration and estimate GHG from the enteric fermentation and manure management in 12 small-scale dairy farms under two feeding strategies. Methodology. Six farms had their herds in confinement under a cut-and-carry feeding system, and six farms implemented day grazing of mixed pastures, both systems used commercial concentrates as a supplement. Cows in milk production and their replacements were considered in the study. Pasture intake was calculated by difference in dry matter intake, using 3.2 % of live weight as intake factor. The N utilisation was determined by difference between N intake and excretion at each farm during a whole year operation. The GHG emissions were estimated following Tier 2 guidelines rom IPCC. Differences in feeding strategies were analysed with a completely random block design using farms as a blocking factor. Results. Mean farm size was 5.0 ha for cut-and-carry and 16.0 ha for grazing, and dry matter feed self-sufficiency was 62 and 83% respectively, considering 12% and 22% refusals for each strategy. There were no statistically significant differences (P>0.05) for any of the N utilisation components (N in diet, N in milk, N in manure, NH3 and N2O or GHG emissions. Implications. This is a novel report on assessing N fluxes and GHG emissions from small-scale dairy systems in Mexico and Latin America. Conclusions. In general, 87.6% of the N consumed is excreted in manure and urine. The feeding strategies did not diverge enough to have an impact on GHG emissions.