High-order numerical techniques and immersed boundary methods (IBMs) are gaining popularity to avoid constructing body-fitted meshes while accurately resolving complex flows on Cartesian grids. Recently, we have presented a new treatment for the immersed boundary method based on the combination of volume penalization and selective frequency damping (SFD) [J. Kou and E. Ferrer, “A combined volume penalization/selective frequency damping approach for immersed boundary methods applied to high-order schemes,” J. Comput. Phys. 472, 111678 (2023).], that offers improved accuracy for nonmoving geometries. The objective of SFD is to remove nonphysical, high-frequency oscillations inside the solid body and by doing so enhance the accuracy in the fluid region. The present paper extends the new immersed boundary treatment to moving geometries. The convergence of this approach is first validated by the method of manufactured solutions, where we design a one-dimensional advection–diffusion case, with a moving interface, to validate the numerical accuracy. Second, we simulate an unsteady flow past a plunging circular cylinder (Navier–Stokes solver). In this case, we show that the combination of volume penalization and SFD provides improved accuracy for moving geometries.