Soybean and peanut are major oilseed crops and important global sources of protein. They also provide significant amounts of carbohydrates and micronutrients. These crops are cultivated worldwide for both human consumption and animal feed. In addition, because of their ability to fix atmospheric nitrogen, soybean and peanut are often used in crop rotations as green manures. However, changing climatic conditions, particularly high temperatures and irregular rainfall during the growing season, adversely affect both yields and seed quality. While numerous studies have been conducted globally to understand and mitigate the effects of heat stress on yield (as reviewed by many research groups), relatively little attention has been given to its impact on nutritional quality. Given the importance of soybean and peanut as major global sources of oil and protein, it is essential to study the effects of heat stress on both harvest quality and final yield. This article examines how heat stress at different developmental stages influences the nutritional quality of soybean and peanut. Additionally, it explores the development and application of lipid, protein, and carbohydrate biomarkers to study and map genes regulating heat stress tolerance in these two crops.