Numerous applications, not only Earth-based, but also space-based, have strengthened the interest of the international scientific community in using Global Navigation Satellite Systems (GNSSs) as navigation systems for space missions that require good accuracy and low operating costs. Indeed, already successfully used in Low Earth Orbits (LEOs), GNSS-based navigation systems can maximise the autonomy of a spacecraft while reducing the burden and the costs of ground operations. That is why GNSS is also attractive for applications in higher Earth orbits up to the Moon, such as in Moon Transfer Orbits (MTOs). However, the higher the altitude the receiver is above the GNSS constellations, the poorer and the weaker are the relative geometry and the received signal powers, respectively, leading to a significant navigation accuracy reduction. In order to improve the achievable GNSS performance in MTOs, we consider in this paper an adaptive orbital filter that fuses the GNSS observations with an orbital forces model. Simulation results show a navigation accuracy significantly higher than that attainable individually by a standalone GNSS receiver or by means of a pure orbital propagation.