Courgette is a popular vegetable belonging to the Cucurbitaceae family. It is known for its good adaptation to different weather conditions, although it performs best in a warm and humid climate. Since the yield and various quality characteristics of vegetables are known to be strongly influenced by a number of weather, agronomic, and genetic (variety/cultivar) factors, in this study we aimed to compare three cultivars of courgette (Atena, Lajkonik and Soraya) grown in two consecutive growing seasons in the organic and conventional agronomic systems. The concentrations of nitrates, nitrites, carotenoids (lutein, zeaxanthin, β-carotene) and chlorophylls (chlorophyll a, chlorophyll b) in courgette fruits were analyzed by HPLC. The growing season had a predominant effect on the yield as well as the majority of the analyzed compositional parameters of the courgette fruits. The studied cultivars differed significantly in the concentration of lutein, β-carotene, and chlorophylls, although some significant interactions between the cultivar and the growing season were observed. On average, organically grown courgettes were characterized by a significantly higher yield, as well as higher dry matter and chlorophyll content, however, this agronomic system’s effect was not consistent among all the studied cultivars in the two seasons. The study suggests that organic practices have a potential to provide high yields of good quality crops, comparable (or, in the case of some parameters, better) than the conventional, resource-intensive horticulture.