High temperature negatively affects plant reproduction and seed yield, posing a challenge for global food security. To better understand the molecular mechanisms underlying the seed heat shock response (HSR), we applied an integrated proteo-transcriptomic approach to analyze gene expression and protein abundance during seed development under long-term heat stress. Our results indicate that transcriptional regulation represents the main driver of the HSR. A positive correlation between transcript and protein abundance suggests that transcriptional upregulation is frequently reflected at the proteome level. Promoter analysis revealed that heat shock transcription factors HSFA1abd and HSFA2 likely regulate a large proportion of heat-induced genes. Binding sites for these factors were detected upstream of most upregulated genes at early stages of seed development. In parallel, we analyzed the contribution of alternative splicing (AS) to the heat stress response. Although widespread AS changes occur during heat stress, their impact on overall mRNA and protein abundance appears limited. Nevertheless, proteomic analyses confirmed the presence of non-canonical protein isoforms generated by alternative splicing, indicating that AS contributes to proteome diversity during the seed heat stress response.