Understanding microalgal responses to subtle temperature changes is critical, as they are primary producers that drive ecosystem productivity and food web dynamics. Even small shifts may alter algal fitness and reshape interactions with other microbes. In this study, C. reinhardtii was grown at non-stress, ambient temperatures of 18 °C and 28 °C. Proteomic analysis of isolated cilia and secreted proteins identified major changes in abundance within these sub-proteomes, particularly intraflagellar transport (IFT) complexes in cilia and mating-related proteins in the secretome that are both upregulated at higher temperature.