Heat stress poses a significant threat to crop productivity; however, the thermotolerance mechanisms in underutilised oilseed crops, such as chia ( Salvia hispanica L.), remain poorly understood. Despite the growing interest in chia as a rich source of ω-3 fatty acids, its molecular response to heat stress, particularly in vegetative tissues, has not been explored. We conducted transcriptomic and lipidomic profiling to examine how chia leaves respond to short-term (3 h) and prolonged (27 h) heat stress (38 °C/20 °C day/night) followed by recovery. Over 20% of transcripts showed differential expression, revealing pathways involving Ca 2+ signalling, heat shock factors, and other stress-related regulators. Almost all heat-responsive genes (>99%) returned to normal levels within 24 hr of recovery, showing a robust restoration of homeostasis. Among 287 annotated lipid species, triacylglycerols exhibited the most significant and reversible changes (>2-fold), suggesting a role in membrane remodelling. These findings highlight the significance of Ca 2+-mediated signalling pathways and molecular chaperones, such as heat shock proteins and heat shock factors, in heat stress adaptation, providing foundational molecular data on chia leaf thermotolerance. This resource enhances our understanding of stress tolerance mechanisms in chia and contributes to broader efforts in developing heat-resilient oilseed crops.