Apricot (Prunus armeniaca L.) is one of the most important members of Prunus and its trees bears delicious and nutritious fruits during summer months in the temperate zones in the world. Apricot cultivars are propagated asexually which consists of clones. Information on inter-clonal variations in apricot cultivars can assist us in the selection of better clones from commercial cultivars. We aimed to determine morphological traits (fruit weight, seed weight, kernel weight, flesh/seed ratio, shape index, fruit firmness, color index), nutritional (sugars and organic acids) and nutraceutical (total phenolic, total flavonoids, total carotenoid and antioxidant activity) composition of 18 clones of Sekerpare apricot cultivar grown together in Kagizman district in eastern Turkey. Results showed significant differences among clones concerning most of the morphological traits, nutritional and nutraceutical compositions. Fruit weight, flesh/seed ratio and fruit firmness of clones were in range of 23.14–27.11 g, 11.21–13.14 and 3.88–5.11 kg/cm2, respectively. Fruit shape index was slightly similar among all clones which was between 0.95 and 1.03. Citric acid and sucrose were found to be the predominant organic acid and sugar among clones which varied from 728 to 915 mg/100 g and 7.11 to 9.94 g/100 g, respectively. The clone ‘KS2’ exhibited the highest level of total phenol (67.1 mg gallic acid equivalent per 100 g) and antioxidant activity (2.16 μmol trolox equivalent per g). The study confirmed the diversity among Sekerpare clones and effectiveness of combining morphological, nutritional and nutraceutical analyses in assessment of Şekerpare clones and its use for future pre-breeding programs.