Griffin, a Multiphysics Object-Oriented Simulation Environment (MOOSE)–based application targeting transient modeling of advanced reactors, has been used recently to model pebble-bed reactors (PBRs). The modeling effort has focused thus far on equilibrium core calculations. A new capability to simulate the running-in phase of PBR operation has been added to Griffin. This work demonstrates the new capability with a coupled multiphysics running-in simulation. Griffin computes power densities in the core at each time step of the running-in simulation and passes these to Pronghorn, which models fluid flow and heat transfer to calculate pebble surface temperatures. These surface temperatures are used along with the power densities in a heat conduction model to compute average fuel and moderator temperatures, which are passed back to Griffin and accounted for with temperature-dependent cross sections. This work also describes a novel methodology for determining appropriate pebble feed rates and control rod positioning during the running-in simulation. The RZ-geometry model used in this work requires minimal computational resources and can be used for optimization and uncertainty studies in future works.