Encystment is a common response of most protists to stress. Although some signaling pathways regulating this process were reported, our knowledge remains limited. Here, we mapped the molecular changes occurring in the amoeba Acanthamoeba castellanii during the early steps of encystment. De novo analysis of the transcriptome identified more than 150,000 previously undescribed transcripts that were utilized for mass spectrometry-based proteomics analysis after triggering starvation. With this strategy, we identified thousands of protein sequences absent from the reference genome. These results revealed the regulation of expected biological processes, such as the shutdown of cell proliferation at transcript level followed by down-regulation of proteins. The phosphoproteome showed a quick regulation of phosphorylation sites involved in cytoskeleton remodeling and translation regulation, among other processes underlying A. castellanii encystment. To our knowledge, this work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource to further investigating amoebae encystment.