Our objective was to determine variables affecting whole-farm balance (WFB) of 2 nutrients [nitrogen (N) and phosphorus (P)] in intensive dairy farms of AguascalientesValley, central Mexico. Eleven farms were selected based on farmer’s willingness to participate. During monthly visits (October 2013 to September 2014), herd structure, milk production, feeding practices and crop-related data were recorded, and samples of milk and forages were collected for N and P analysis. Annual WFB were calculated as Purchased inputs (feeds + fertilizers + animals) – sold outputs (milk + animals). Biological N fixation was not considered and none of the farms surveyed exported manure or crops. Explanatory variables included animal unit (AU = 454 kg of live-weight), animal density (AD = AU/ha of tillable land), on-farm forage dry matter (DM) production [OFP (%) = 100 x OFP (Mg)/(OFP (Mg) + forage DM purchased (Mg))], on-farm nutrient production [ONP (%) = 100 x ONP (Mg)/(ONP (Mg) + feed nutrient purchased (Mg))], and nutrient conversion efficiency [NCE (%) = 100 x nutrient output (Mg)/(ONP (Mg) + feed nutrient purchased (Mg))]. Descriptive statistics and multivariate regression using forward stepwise selection were obtained with R. Milking cows was (mean ± SD) 623 ± 582, AU was 1372 ± 1379, tillable land was 109 ± 85 ha (19.7 ± 34.2 ha of alfalfa and 89.5 ± 76.2 ha of corn and other annual crops), AD was 13 ± 6.2 AU/ha, and OFP was 81.2 ± 21.3%. In addition, ONP was 43.6 ± 13.6% and 37.1 ± 15.6%, and NCE was 25 ± 4 and 31 ± 11% for N and P, respectively. Feed nutrient purchased was 70.4 and 83.1% of purchased inputs for N and P respectively. Milk output was 11,229 ± 1,236 kg/cow/yr. The WFB was 80,558 ± 70,604 and 14,080 ± 13,453 kg/yr, 832 and 141 kg/ha, 69 and 12 kg/AU, and 13 and 2.3 kg/Mg of milk, for N and P respectively. For both N and P, WFB (kg/ha, kg/AU and kg/Mg of milk) was associated negatively with OFP and NCE (all P ≤ 0.05). For the intensive dairy farms of this study, WFB were unusually large, but our findings that increasing OFP and NCE contributed to lowering WFB was consistent with other studies.