Nuclear technologies have the potential to play a unique role delivering low carbon energy for a future net-zero society. However, for the long-term success, nuclear will need to deliver innovative solutions as proposed in iMAGINE. One of the key challenges for the envisaged highly integrated nuclear energy system is the need for a demand driven salt clean-up system. The work described provides an insight into the interplay between a potential salt clean-up system and the reactor operation in a dynamic approach. The results provided will help to optimize the parameters for the salt clean-up process by delivering a dynamically calculated priority list identifying the elements with high influence on reactor operation. The integrated model is used to investigate the ideal time for the initiation of the clean-up as well as the effect of different throughput through the clean-up system on criticality as well as on the concentration of the elements in the reactor salt. Finally, a staggered approach is proposed with the idea to phase in the chemical clean-up processes step by step to keep the reactor critical. The results provide an essential step for the progress of iMAGINE as well as the basis for the inter disciplinary work required to bring iMAGINE into real operation.