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Purpose Thistle flower (Cynara cardunculus) aqueous extracts, as rich source of milk-clotting peptidases, have been widely used for cheeses marketed under the Registry of the Protected Designation of Origin, as it is the case of Serra da Estrela cheese, manufactured from raw ewes’ milk and without addition of any commercial starter culture. This paper aims at studying the influence of six different ecotypes of thistle flowers in cheese properties during the ripening and of final products.Design/methodology/approach Cheeses were produced with different thistle flower extracts and then the clotting time, weight and colour of cheeses, as well as texture properties and sensorial characteristics, were evaluated.Findings The clotting time varied from 47 to 66 min, and the weight loss along ripening varied between 32 and 40 per cent. There was some influence of thistle flower ecotype on the colour during ripening and in the final product. The results of texture analysis revealed significant differences between the thistle ecotypes: crust firmness varying from 2.4 to 5.6 N; inner firmness from 0.82 to 1.82 N; stickiness from −0.5 to −1.60 N; adhesiveness from −3.0 to −11.3 N.s; and Ecotype C was particularly distinguishable. Sensorial evaluation revealed differences among the cheeses, with Ecotype C receiving the highest score for global appreciation.Originality/value The usage of different extracts of thistle flower to produce Serra da Estrela cheese with different properties is a novelty, and it allows the possibility of manipulating this parameter in the future so as to produce cheeses with specific characteristics, addressed to different consumer targets. [ABSTRACT FROM AUTHOR]