Griffin, a MOOSE (Multiphysics Object-Oriented Simulation Environment) based application targeting transient modelling of advanced reactors, has been used recently to model pebble-bed reactors (PBRs). The modelling effort has focused thus far on modelling the equilibrium core. A new capability to simulate the running-in phase of PBR operation has been added to Griffin. This work demonstrates the newcapability with a sample multiphysics running-in simulation. The basic features of the new running-in capability were documented previously; however, the sample simulation results presented there did not include multiphysics; the fuel temperatures were assumed to be constant. In this work, Griffin computes power densities in the core at each timestep of the running-in simulation and passes these to Pronghorn which models fluid flow and heat transfer to calculate temperatures that are passed back to Griffin and accounted for with temperature dependent cross-sections.