Apples are seasonal fruits, and thus after harvesting apples of optimal picking maturity, it is important to prepare them properly for storage and to ensure proper storage conditions in order to minimize changes in the chemical composition and commercial quality of the apples. We studied the quantitative composition of triterpenic compounds in the whole apple, apple peel and apple flesh samples before placing them in the controlled atmosphere (CA) chambers, and at the end of the experiment, 8 months later. HPLC analysis showed that highest total amount of triterpenic compounds (1.99 ± 0.01 mg g−1) was found in the whole apple samples of the ‘Spartan’ cultivar stored under variant VIII (O2—20%, CO2—3%, N2—77%) conditions. Meanwhile, the highest amount of triterpenic compounds (11.66 ± 0.72 mg g−1) was determined in the apple peel samples of the ‘Auksis’ cultivar stored under variant II (O2—5%, CO2—1%, N2—94%) conditions. In the apple peel samples of the ‘Auksis’ cultivar stored under variant I (O2—21%, CO2—0.03%, N2—78.97%) conditions, the amount of individual triterpenic compounds (ursolic, oleanolic, corosolic, and betulinic acids) significantly decreased compared with amount determined before the storage. Therefore, in the apple flesh samples determined triterpenic compounds are less stable during the storage under controlled atmosphere conditions compared with triterpenic compounds determined in the whole apple and apple peel samples.