It is widely assumed that women's empowerment plays a key role in achieving sustainability in agriculture. However, there is a lack of empirical analysis to support this claim and operationalise the concept of women's empowerment. Furthermore, it has not been formally demonstrated through which farming practices women's empowerment can contribute to the development of sustainable agriculture, or whether gender empowerment is indeed meaningful compared with other well‐documented social drivers. We calculated frontier eco‐efficiency, taking into account specific environmental pressures (i.e., soil biodiversity loss) and public goods (i.e., plant diversity) as desirable outputs in small crop farms, which dominate in Central and Eastern European countries (Poland, Romania, Serbia and Moldova), based on a survey conducted in a sample of 1630 units. We estimated the impact of different levels of women's and men's empowerment on eco‐efficiency in the context of other time‐invariant socio‐economic factors (i.e., succession, age, education and specialisation) in a two‐stage double‐bootstrapped Data Envelopment Analysis (DEA) approach. A set of four levels of gender empowerment was defined, taking into account social participation and decision‐making power. We then assessed the degree of input and output inefficiency associated with each level of gender empowerment. The general conclusion is that lower levels of women's empowerment have a negative impact on eco‐efficiency. Therefore, the issue of gender empowerment, not only in terms of equality, decision‐making and access to resources, but also in terms of social participation, should be emphasised in sustainable agriculture policies, on a par with the issue of ageing farmers and farm succession.