Localisation by Reduction and Reconstruction (LoRRe) is a new method to map RNA and protein subcellular distribution in membrane and membraneless compartments like stress granules. Importantly, all RNA subcellular locations are interrogated simultaneously, enabling proportional localisation of each RNA. Using LoRRe, we obtain the first global overview of RNA and protein re-localisation during the unfolded protein response (UPR). Despite the global translation shutdown, actin cytoskeleton RNAs maintain ER localisation via eIF3D binding. Codon usage and membrane-localisation are discovered to be important features for targeting RNA to granules, and new proteins regulating this process are identified. Overall, the RNA and protein localisation data provides the most comprehensive picture to date of macromolecule subcellular localisation and re-localisation under stress conditions.