The interest on embedded boundary methods increases in Computational Fluid Dynamics (CFD) because they simplify the mesh generation problem in the case of the Navier-Stokes equations. The same simplifications occur for the simulation of multi-physics flows, the coupling of fluid-solid interactions in situation of large motions or deformations, to give a few examples. Nevertheless an accurate treatment of the wall boundary conditions remains an issue of the method. In this work, the wall boundary conditions are easily taken into account through a penalization technique, and the accuracy of the method is recovered using mesh adaptation, thanks to the potential of unstructured meshes. Several classical examples are used used to demonstrate that claim.