Anaesthesia has been used for centuries for medical purposes. With the application of anaesthesia, organisms lose their conscious awareness. It provides a temporary loss of sensation, which enables painless performance during surgery. However, the cellular mechanisms underlying the effects of anaesthesia are not clearly understood. It has been proposed that plant root function is analogous to the human brain. Here, using super-resolution imaging technique, we explored an organelle-level understanding of the effect of anaesthesia on plant roots and the stem connecting to the root. Our results showed that the nuclei organized themselves in an orchestrated manner upon treatment with both local and general anaesthesia without damaging their structure. Euchromatin within the nucleus was found to be reorganized in the nuclear periphery, and this process was found to be independent of ATP. In contrast, mitochondria, microtubules, endocytic vesicles, and chloroplasts, which are other important organelles in plant cells, were highly altered or damaged under the same experimental conditions. Eventually, the cellular homeostasis again maintained and process is reversible upon the removal of anaesthesia. Our results suggest that such orchestrated chromatin organization without disturbing the overall structure of the nucleus could be used as a potent biomarker for conscious awareness in plants.