Plants are sessile organisms adapting constantly to environmental fluctuations through spatial and temporal transcriptional responses. We used the latest generation of MS2 RNA labelling system combined with microfluidics to monitor impact of modification of phosphate supply by live transcription imaging. MS2/MCT system is based on a fusion between GFP and the coat protein of bacteriophage MS2 (MCP-GFP), which recognizes a specific RNA stem-loop inserted in multiple copies into a reporter RNA. This enabled quantitative measurements of the transcriptional activity of single loci in living Arabidopsis plants, providing direct visualization of transcriptional regulation within entire organs. Using phosphate responsive genes as model, we found that active genes displayed high transcription initiation rates and frequently clustered together in endo-replicated cells. We also observed large differences between alleles of single cells and in agreement, intrinsic noise was larger than extrinsic variations. Moreover, we established that the transcriptional repression triggered in roots by phosphate, a crucial macronutrient limiting plant development, occurred with unexpected fast kinetics in the range of minutes, and with striking heterogeneity between neighboring cells. Access to single cells RNA polymerase II dynamics within live plants will benefit the study of numerous signaling processes.