To the better management of spring frost problem in the apricot cultivars, evaluation of biochemical changes in flower and/or flower organs during bud break could be one of the key factors. In this study, the relationship between the biochemical metabolites such as amino acids and minerals in the receptacle and pistil organs of two different apricot cultivars (frost-sensitive and frost-tolerant) and their relative effects on the frost tolerance of the cultivars and their organs were investigated during full blooming stage. In both apricot cultivars, it was found that the cell death points (CDP) of flower receptacle (− 6.3 to − 8.4 °C) were at higher temperatures than the CDP of flower pistil organs (− 13.1 to − 14.5 °C). Receptacle organs in flower, therefore, had less tolerance to spring frost damage. In addition, significant differences in mineral and amino acid contents were detected both between apricot cultivars and between the receptacle and pistil organs of the cultivars. Amino acid and mineral contents were lower both in the freezing-sensitive apricot cultivar (“Mihralibey”) and the freezing-sensitive organ (receptacle) in comparison with the freezing-tolerant apricot cultivar (“Iğdır Şalak”) and the freezing-tolerant organ (pistil). A significant negative correlation was also observed between the mean CDP values and both amino acid and mineral contents in the receptacle and pistil organs of both apricot cultivars. A negative correlation was found between CDP values and glutamate from amino acids and N, K, and Mg from minerals, and also these were determined that they had positive effects on frost tolerance increase. An important finding from our work revealed that the amount of each mineral and amino acid allocated differently to the receptacle and pistil organs of the apricot cultivars. The understanding of the amino acids and the mineral dynamics may contribute to improving the tolerance of flowers of apricot or other deciduous species to frost damage during spring. In the future, we may conclude that protection strategies such as increasing amino acids and mineral content in the receptacle organ of flowers would be necessary to cope with the negative effects of spring frost.