In this study, the effect of spermidine (SP) treatments at different doses after harvest on the changes in the pomological and biochemical contents of nectarine fruits was determined. The fruits were placed in cold storage (4 ± 0.5 °C and 90 ± 5% RH) for 30 days. Specific organic acids and phenolic compounds from biochemical compounds were analyzed by HPLC device. Weight loss and decay values, which are quality criteria of nectarine fruits, increased during storage compared to the harvest period. In this study, 1.0 mM SP application was found to be more successful in the preservation of visual quality (fruit pulp firmness and weight loss) properties during storage. At the end of the storage period (30th day), weight loss was determined as 3.27% in the control group and 1.84% in the 1.5 mM SP treatment. Fruit flesh firmness value, which is one of the important quality parameters affecting the storage life of fruits, was determined as 30.97 N in the control group and 37.06 N in 1.5 mM SP doze (30th day). Contrary to the acidity values, the total soluble solids content (TSS) and fruit juice pH values increased during storage. In this research, when the organic acid and phenolic compound contents are examined; it was determined that the dominant organic acid and phenolic compound in nectarine fruits were malic acid and chlorogenic acid, respectively. The malic acid ratio was found to be 4.89 g/kg in the control group and 6.66 g/kg in 1.5 mM SP treatment at the end of the 30-day storage period. Chlorogenic acid content was recorded as 6.86 mg/100g in the control group and 8.82 mg/100g in 1.5 mM SP application at the end of the storage period (30th day). In this study, it was determined that a 1.5 mM SP dose after harvest was effective on the biochemical contents of nectarine fruits and protected the fruits more during storage.