The one-particle reduced density-matrix (1-RDM) functional theory is a promising alternative to density-functional theory (DFT) that uses the 1-RDM rather than the electronic density as a basic variable. However, long-standing challenges such as the lack of the Kohn–Sham scheme and the complexity of the pure N-representability conditions are still impeding its wild utilization. Fortunately, ensemble N-representability conditions derived in the natural orbital basis are known and trivial such that almost every functional of the 1-RDM is actually natural orbital functional, which does not perform well for all the correlation regimes. In this work, we propose a variational minimization scheme in the ensemble N-representable domain that is not restricted to the natural orbital representation of the 1-RDM. We show that splitting the minimization into the diagonal and off-diagonal parts of the 1-RDM can open the way toward the development of functionals of the orbital occupations, which remains a challenge for the generalization of site-occupation functional theory in chemistry. Our approach is tested on the uniform Hubbard model using the Müller and the Töws–Pastor functionals, as well as on the dihydrogen molecule using the Müller functional.