Steadily more extreme heatwaves threaten crop production worldwide, primarily through reduced viability of gametes. The formation of male gametophytes is particularly susceptible to temperatures above ~36°C. We report here on molecular events that characterise male gametophytes as they develop under specific heat regimes and identify potential approaches for crop improvement. Cotton was used as a relatively heat-tolerant species to demonstrate compromised pollen function. Gametophytes were exposed to moderate (36/25°C, day/night) and extreme heat (38/28°C and 40/30°C) for five days, coinciding with meiosis (tetrads) and mitosis (uninucleate and binucleate microspores) and pollen maturation. Morphological and physiological changes were analysed alongside molecular responses in each developmental stage. Severe cell damage was observed when tetrads were exposed to 40/30°C, resulting in failed dehiscence, smaller pollen grains, and yield loss. Molecular analysis demonstrated that each stage of pollen development has qualitatively distinct transcriptome and proteome profiles. Notably, extreme heat induced unique expression patterns in tetrads, in contrast with the relatively heat-tolerant mature pollen and leaves. We demonstrated that although molecular chaperones were abundant during meiosis, where they putatively refold aggregated proteins, they were not highly up-regulated in the late stages of pollen development. We speculate that accelerated metabolism contributes to the susceptibility of meiotic cells to heat. Identifying the precise molecular events underlying the susceptibility of gamete formation to heat is a challenging but vital goal for plant (and animal) research.