Legumes are important crop species as they produce highly nutritious seeds for human food and animal feed. In grain legumes, sub-optimal conditions affect seed developmental timing leading to impairment of seed quality traits acquired during seed maturation. To understand the molecular mechanisms of heat stress response in legume seeds, we analysed transcriptome changes of three seed tissues (i.e. em bryo, endosperm and seed coat) at four developmental stages, during seed maturation, from seed filling to mature dry seeds, collected under optimal and heat stress conditions in the model legume, Medicago truncatula (reference genotype A17). The total RNA sequencing generated a dataset of 48 samples, representing more than 57 Gb fastq raw data. Mapping, quantification and annotation of the data were based on fifth release of Medicago truncatula genome and provided expression profiles of 44,473 transcripts in seed tissues at different developmental stages and under optimal and stress conditions. Time-course and pairwise comparisons between optimal and stress conditions showed that 9182, 8315 and 3481 genes were differentially expressed due to heat stress in embryo, endosperm and seed coat respectively. Moreover, it highlighted a common set of 975 genes that were differentially expressed in all the seed tissues.