A temporal homogenization approach for the numerical simulation of atherosclerotic plaque growth is extended to fully coupled fluid‐structure interaction (FSI) simulations. The numerical results indicate that the two‐scale approach yields significantly different results compared to a simple heuristic averaging, where only stationary long‐scale FSI problems are solved, confirming the importance of incorporating stress variations on small time‐scales. In the homogenization approach, a periodic fine‐scale problem, which is periodic with respect to the heart beat, has to be solved for each long‐scale time step. Even if no exact initial conditions are available, periodicity can be achieved within only 2–3 heart beats by simple time‐stepping.