This study aimed to investigate the changes in the pecan kernel color, carotenoids, polyphenols, and physicochemical properties during five months of storage at room temperature for five different pecan varieties. The results showed that the pecan kernel color darkened with a shift toward more red and less yellow during the storage. Additionally, the dorsal side of the kernel had a lighter color than the ventral side. Total carotenoids deceased from 92.0−118.8 to 45.2−101.9 μg/100 g of whole kernel, while total polyphenols had no significant differences (18.1−27.0 mg of GAE (gallic acid equivalent)/g of whole kernel) commonly. Three phenolics (gallic acid, catechin, and ellagic acid) were of 6. 7−9.6, 31.4−46.7, and 11.7−16.2 mg/100 g of whole kernel and increased during storage. The pecan kernel moisture loss was significant, while the total lipids remained unchanged. Five texture parameters (hardness, toughness, slope, fracturability, and break) showed irregular changes. Genotypic variation was observed in all five varieties, although the storage was the main factor affecting the compositions.