Large-scale coherent structures emerging in two-dimensional flows can be predicted from statistical physics inspired methods consisting in minimizing the global enstrophy while conserving the total energy and circulation in the Euler equations. In many situations, solid obstacles inside the domain may also constrain the flow and have to be accounted for via a minimum enstrophy principle. In this work, we detail this extended variational formulation and its numerical resolution. It is shown from applications to complex geometries containing multiple circular obstacles that the number of solutions is enhanced, allowing many possibilities of bifurcations for the large-scale structures. These phase change phenomena can explain the downstream recombinations of the flow in rod-bundle experiments and simulations.