Elevated temperatures resulting from climate change are adversely impacting natural and crop ecosystems, necessitating the development of heat-tolerant crops. To identify regulators of high temperature stress signalling that are conserved in flowering plants, we mapped changes in protein phosphorylation in both dicots and monocots exposed to elevated temperature. In addition, we established a framework to precisely identify protein-phosphorylated sites associated with varying temperature sensitivities. First, our findings demonstrate that the phosphorylation state of a specific set of proteins creates a unique signature for heat stress tolerance. Second, we identified MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE4 (MAP4K4)/TARGET OF TEMPERATURE3 (TOT3) as a conserved regulator of thermomorphogenesis and stomatal opening, and we unravelled a part of the signalling network that controles these processes. Taken together, our findings aid the identification of targets for breeding or genome editing to enhance heat tolerance and can contribute to ensuring food security under a changing climate.