The cardoon (Cynara cardunculus L.) is a mandatory vegetable coagulant for certain Protected Designation of Origin Portuguese cheeses. It grows wild in Portugal and is used without any type of control regarding flower picking or extract preparation, representing some uncertainty in cheese manufacture. The variability in technological properties, in the context of traditional cheese manufacture, of cardoon flower ecotypes from the Alentejo region was evaluated, including milk clotting and proteolytic activities, coagulation properties and potential cheesemaking yield of flower extracts. Multivariate statistics highlighted the variability of flower properties for cheesemaking, but allowed the aggregation of the ecotypes into five groups under the major influence of milk clotting activity and effect on gel firmness and micellar aggregation rate, followed by proteolytic activity. These differences may have an impact on cheese properties and therefore can allow the selection of cardoon flower for the manufacture of different types of cheese.