The properties of an F=1 spinor Bose-Einstein condensate trapped in a double-well potential are discussed using both a mean-field two-mode approach and a simplified two-site Bose-Hubbard Hamiltonian. We focus in the region of phase space in which spin effects lead to a symmetry breaking of the system, favoring the spatial localization of the condensate in one well. To model this transition we derive, using perturbation theory, an effective Hamiltonian that describes N/2 spin singlets confined in a double-well potential.