We present a Fourier pseudo-spectral method for solving the resistive magnetohydrodynamic equations of incompressible flow in confined domains. A volume penalisation method allows to take into account boundary conditions and the geometry of the domain. A code validation is presented for the z-pinch test case. Numerical simulations of decaying MHD turbulence in two space dimensions show spontaneous spin-up of the flow in non-axisymmetric geometries, which is reflected by the generation of angular momentum. First results of decaying MHD turbulence in a cylinder illustrate the potential of the new method for three-dimensional simulations.