BACKGROUND: Lentil, a cool-season food legume, is highly sensitive to high temperatures, which drastically reduce biomass and seed yield. The effects of heat stress on qualitative and quantitative aspects of seeds are not yet known. RESULTS: In this study, we assessed the effects of high temperatures on quantitative and qualitative aspects of seeds in a heat-tolerant (HT; FLIP2009) and heat-sensitive (HS; IG4242) genotypes in a controlled environment. Initially, the plants were raised in a natural, outdoor environment (22/10 °C mean day/night temperature, 1350 µmol m−2 s−1 light intensity, 60–65% relative humidity) from November to mid-February until 50% flowering (114–115 days after sowing). After that, one set of plants was maintained in a controlled environment (28/23 °C, as mean day and night temperature, 500 µmol m−2 s−1 light intensity, 60–65% relative humidity;control) and one set was exposed to heat stress (33/28 °C, as mean day and night temperature, 500 µmol m−2 s−1 light intensity, 60–65% relative humidity), where they remained until maturity. Compared to control, heat stress reduced the seed growth rate by 30–44% and the seed-filling duration by 5.5–8.1 days, which ultimately reduced the seed yield by 38–58% and individual seed weights by 20–39%. Heat stress significantly damaged cell membranes and reduced chlorophyll concentration and fluorescence, and the photosynthetic rate, which was associated with a significant reduction in relative leaf water content. The proximate analysis of seed reserves showed that heat stress reduced starch (25–43%), protein (26–41%) and fat (39–57%) content, and increased total sugars (36–68%), relative to the controls. Heat stress also inhibited the accumulation of storage proteins including albumins, globulins, prolamins and glutelins (22–42%). Most of the amino acids decreased significantly under heat stress in comparison to control, whereas some, such as proline, followed by glycine, alanine, isoleucine, leucine and lysine, increased. Heat stress reduced Ca (13–28%), Fe (17–52%), P (10–54%), K (12.4–28.3%) and Zn (36–59%) content in seeds, compared to the controls. CONCLUSIONS: High temperatures during seed filling are detrimental for seed yield and quality components in lentil genotypes, with severe impacts on heat-sensitive genotypes.