There is widespread recognition of the global environmental impact of agricultural production on greenhouse gas emissions, but evidence is sparse regarding the impact in the Middle East and North Africa (MENA) region. In this study, we treat agricultural emissions as an undesirable output from agricultural production and apply the directional distance function to measure environmentally-adjusted technical efficiency, defined as environmental efficiency in agricultural production, in six countries in the MENA region (Algeria, Egypt, Israel, Jordan, Morocco, Tunisia) during the period 1980–2016. The results show that all six countries have clear scope to improve their environmental efficiency. Agricultural production is greener in Jordan and Israel, while environmental efficiency is currently lowest in Egypt and Morocco. Estimated relative shadow price of agricultural emissions is −1.002, implying that the ‘cost’ of removing agricultural emissions is almost equal to the value of producing one unit of good output. These findings suggest there is a trade-off between agriculture emissions and production, which should be considered in efforts to enhance the sustainability of agricultural production in the MENA region.