Abstract For BepiColombo's five-year journey into the inner solar system, a combination of low-thrust arcs and six flybys (one at Moon and Earth, two at Venus and two at Mercury) will be used to reach Mercury with low relative velocity. At arrival a gravitational capture approach is foreseen, in which the Sun perturbation is exploited to get weakly captured around Mercury for a number of orbits. This trajectory imposes severe constraints from a navigational point of view. Very precise navigation is required due to the low flyby altitudes planned for Venus (300 km) and Mercury (200 km) and the level of accuracy needed for the final arrival through the vicinity of the Sun–Mercury L1 point. Besides that, the solar plasma effect severely degrades the quality of the radiometric measurements near superior solar conjunctions, which are more frequent for missions to the inner solar system. Moreover, perturbations, as the ones introduced by momentum wheel desaturation burns, entry into safe modes or solar radiation pressure, must also be taken into account. Delta-differential one-way range measurements are found to be required in periods of poor orbit determination prior to some gravity assists. Nevertheless, if a safe mode is triggered at a critical moment that produces a change in velocity in an unfavourable direction, the mission could be jeopardised. To avoid that risk, an increase in the flyby altitude and possibly a partial or total redesign of the trajectory to avoid flybys near solar conjunctions are considered.