In many earth science and environmental problems, the fluid-structure interactions can affect the hydrodynamics properties of the porous medium via the spatial evolution of its solid matrix. A significant insight into these properties can be obtained from pore-scale simulations. Using a 3D pore-scale domain with moving walls, we proposed in this paper a comparison of the numerical accuracy between different approaches in regard to flow and reactive transport. Two direct-forcing immersed boundary (IB) models coupled with lattice Boltzmann method (LBM) are evaluated for the flow calculation against an analytical solution. The IB-LBM showed improvement compared to the classical and interpolated bounce-back lattice Boltzmann model. Concerning the reactive transport, the most accurate IB-LB method was coupled with two non-boundary conforming finite volume methods (volume of fluid and reconstruction). The comparative study performed with different mesh sizes and Damkohler numbers demonstrates better results for the reconstruction method.