In this study environmental efficiency of main root crop (sugar beets and potatoes) cultivation in Poland is evaluated. Survey data from 62 sugar beet and 74 potato farms in the years 2016 and 2017 were used for analysis. To assess efficiency, the slack based Data Envelopment Analysis model (SBM-DEA) was used, where greenhouse gas emissions were assumed as undesirable output. The reasons for inefficiency in cultivation were explained using the fractional regression model (FRM), with habitat and organizational conditions as independent variables. Differences in the structure of greenhouse gas emissions from the crops under study were indicated as a result of differences in technology used at each farm. The estimated average carbon footprint on the analysed farms for sugar beet cultivation was 0.057 (±0.042) kg CO2 e/kg and 0.13 (±0.17) kg CO2 e/kg for potato cultivation. The obtained results indicate that effective farms growing sugar beet emit, on average, 14.5% less greenhouse gases, achieving a slightly higher yield. In potato cultivation, this reduction is 15.3% with a 27% increase in yield. It has been shown that weather conditions and the economic size of farms can significantly affect the environmental efficiency of both analysed crops.