The use of the variational quantum eigensolver (VQE) for quantum chemistry is one of the most promising applications for noisy intermediate-scale quantum (NISQ) devices. A major limitation is represented by the need to build compact and shallow circuit ansatzes having the variational flexibility to catch the complexity of the electronic structure problem. To alleviate this drawback, we introduce a modified VQE scheme in which the form of the molecular Hamiltonian is adapted to the circuit ansatz through an optimization procedure. Exploiting the invariance of the Hamiltonian by molecular orbital rotations, we can optimize it using gradients that can be calculated without significant computational overload. The proposed method, named Wavefunction Adapted Hamiltonian Through Orbital Rotation (WAHTOR), has been applied to small molecules in numerical state vector simulations. The results demonstrate that, at variance with standard VQE, the method is less dependent on circuit topology and less prone to be trapped into high-energy local minima. It is able to recover a significant amount of electron correlation even with only empirical ansatzes with shallow circuit depth. Noisy calculations demonstrate the robustness and feasibility of the proposed methodology and indicate the hardware requirements to effectively apply the procedure using forthcoming NISQ devices.