Tensor network states and specifically matrix-product states have proven to be a powerful tool for simulating ground states of strongly correlated spin models. Recently, they have also been applied to interacting fermionic problems, specifically in the context of quantum chemistry. A new freedom arising in such non-local fermionic systems is the choice of orbitals, it being far from clear what choice of fermionic orbitals to make. In this work, we propose a way to overcome this challenge. We suggest a method intertwining the optimisation over matrix product states with suitable fermionic Gaussian mode transformations. The described algorithm generalises basis changes in the spirit of the Hartree-Fock method to matrix-product states, and provides a black box tool for basis optimisation in tensor network methods.