Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and epigenetic changes on three stages of seed development and two stages during seed germination. By analyzing candidate epigenetic markers using the mutants’ physiological assays, we observed that DNA methylation and histone marks greatly participate into the acquisition of seed germination quality traits, especially when seeds have been produced under stressful conditions. To illustrate this process, Arabidopsis Col‐0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination‐related genes, including a UTR region of a recently identified genes involved in the seed germination plasticity, called MIEL1. To conclude, our results indicate that changes in DNA (de)methylation and histone marks could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress.