For some types of seafood, such as clams, there are now sustainability certificates that guarantee their sustainable production. However, their consumption may be associated with some ethical and sustainability concerns, as clams are harvested in ways that may be harmful to the environment. The aim of this study is therefore to investigate consumers’ sustainability concerns based on their purchasing preferences and WTP for clams with sustainability certification in three Mediterranean countries—Italy, Spain and Croatia. Data were collected online and consumer preferences were elicited using a labelled discrete choice experiment. The results show that in general all consumers prefer clams from their country of origin, while there are differences in their appreciation for the sustainability certification. While Croatian consumers are not very interested in the current Marine Stewardship Council (MSC) sustainability certification, consumers in Spain are willing to pay a higher price for it. At the same time, consumers in Italy are more interested in new certifications such as Responsible Fisheries Management (RFM). These results could be of interest to clam production and distribution companies trying to advance their corporate social responsibility activities and positioning.