This work was focused on measuring environmental inefficiency in Mexican dairy farms, considering climate change variables related to the emission of greenhouse gases (GHG) and planetary geomagnetic activity. The applied methodology measures the eco-efficiency of Mexican dairy farms using the empirical application of a stochastic frontier model of the bioeconomy. The productive sector of the bioeconomy studied was the eco-intensification of the livestock production system (dairies). The environmental inefficiency effect was assumed to be a distribution-independent truncation of a normal distribution with constant variance, while the mean was a linear environmental function of the observable variable. The results showed that the coefficients of the frontier model were highly significant, highlighting the investment in livestock (50%). The inefficiency model had an impact on climate variation with greenhouse gas emissions CH4 (1.96%). The results of the environmental technical efficiency in geometric average were 81.28%. The producers that reached the border with a technical efficiency equal to 1 are the references for the rest, marking the relative technical efficiency. It was concluded that the coefficients in the model were very significant, showing the level of investment in livestock (50%). The low-performance model estimates the impact of climate change on GHG emissions CH4 (1.96%) explaining the trend of increasing GHG emissions, keeping in view that the management of food and cattle during the study period were affected by summer feeding, which allowed considering the activity of GHG emissions. According to the results, the geometric mean environmental performance of engineering is 81.28%.