The improvement of existing analyses that access the physiological quality of seeds and the inclusion of nondestructive techniques represent significant progress to the seed sector. Despite being prominent, the use of x‐ray is hindered by the fact that radiographic images are, in general, analyzed subjectively. Therefore, this study aimed at investigating the relationship between the seed internal morphology, accessed via x‐ray images, and the physiological quality of habanero pepper seeds. The seeds were harvested from fruits at three maturity stages and then kept in post‐harvest storage for different periods. Initially, radiographs were generated and subjected to automated image analysis, using the ImageJ software. The parameters area, perimeter, circularity, relative density, integrated density, and percentage of seed filling were evaluated. After the x‐ray testing, the seeds were tested for germination and vigor. It was observed that postharvest storage increased the relative density of seed tissues, as well as seed filling and germination for all stages of maturity. Positive and significant correlations were found between tissue density parameters, evaluated by image analysis, with seed germination, germination speed and seed viability, while negative correlations were observed with seed dormancy. In general, the automated radiograph analysis of habanero pepper seeds is a promising method to obtain physical variables of seeds, such as relative density, integrated density, and seed filling. Habanero pepper seeds obtained from yellow and orange fruits exhibit higher physiological quality. The storage of these fruits after harvested before seed extraction is a good alternative to improve the seed physiological quality.