In recent years, the certification of environmental sustainability has been adopted by a large number of farms. A wide range of recent literature proved consumers’ preference and willingness to pay (WTP) for certification claiming for reduced environmental impact of food production, whereas the literature on farmers’ preference for a specific scheme design is scant. This study aims at investigating the possibilities of developing an environmental certification (EC) for agricultural products that is more tailored to farmers’ expectations. Data from an original survey among 116 producers from Italy, Croatia, and Greece were used to investigate the most preferred elements of a hypothetical EC for a general agricultural product, by means of a choice experiment. Although differences emerge in relation to the nationality of respondents, the results on average suggest a clear preference and a higher WTP by farmers for a certification that may guarantee an efficient use of water resources. Furthermore, farmers are found to be more inclined toward a public certifying body and the possibility to receive technical assistance for the scheme adoption.