The impact of the extraction technique and genotype on the oil yield and profile/concentration of fatty acids, tocopherols, sterols, and squalene in oil obtained from the seeds of three Japanese quince (Chaenomeles japonica) cultivars (“Rondo,” “Darius,” and “Rasa”) are studied. The oil recovery from Japanese quince seeds is affected by two factors; extraction technique, and genotype. The lowest oil recovery is recorded for the cold‐press method and cv. “Rondo,” and the highest for ultrasonic extractions and cv. “Rasa.” The profile of fatty acids in Japanese quince seed oil is dominated by three fatty acids C18:2, C18:1, and C16:0. The extraction method does not impact fatty acid and tocopherol composition as well as squalene content, as opposed to genotype, which has a statistically significant impact. The composition of tocopherols in the Japanese quince seed oil is dominated by the α‐T (97%), while the β‐T and γ‐T constituted only minor level (below 2% of each). The extraction type and genotype have a significant impact on the composition of the most of sterols. Regardless of the type of extraction and genotype, the β‐sitosterol consists of over 80% of total sterols in Japanese quince seed oil. The plant genotype is the key factor, which determines the profile of the fatty acids and the concentration of bioactive compounds in the extracted oil from Japanese quince seed, while the extraction technique plays a secondary role.Practical Applications: The agro‐industrial by‐products generated by the fruit industry, for example, seeds, continue to rise year to year. One of the more popular processed fruit crop is Japanese quince (Chaenomeles japonica). This study demonstrates the impact of the extraction technique (four methods of extractions: cold‐pressing, supercritical CO2 fluid, ultrasound‐assisted, and Soxhlet) and genotype (three cultivars “Rondo,” “Darius,” and “Rasa”) on oil yield, fatty acid profile, and concentration of tocopherols, sterols, and squalene. Provided information can help with more efficient utilization of the tonnes of seeds generated by the fruit industry and consequently contributing to the more effective use of harvested plant material as well as health, economic, and environmental benefits.The impact of the extraction technique and genotype on the oil yield and profile/concentration of fatty acids, tocopherols, sterols and squalene in oil obtained from the seeds of three Japanese quince (Chaenomeles japonica) cultivars (“Rondo,” “Darius,” and “Rasa”) are studied. The plant genotype is the key factor which determines the profile of the fatty acids and the concentration of bioactive compounds in the extracted oil from Japanese quince seed, while the extraction technique plays a secondary role.