His father, the governor of the Mascarene Islands, died in 1778 and left his son his estate of Médine on Mauritius, from which Magon derived his full name.

He fought in three battles against Rodney's fleet off Dominica before serving in de Grasse's squadron on the Caton, fighting at the Chesapeake, St. Kitts and Les Saintes.

On 1 May 1786 he was promoted to lieutenant de vaisseau and in November 1786 he was put in command of the frigate Amphitrite, with which he recaptured Diego Garcia from the British.

On arriving back in Paris he had his property confiscated on being accused of colluding with Malartic in disallowing the French Directory agents Baco de la Chapelle and Burnel from applying the decree of 16 Pluviôse Year II on the abolition of slavery[1] (revoked by the Law of 20 May 1802) but instead forcibly re-embarking them for France.

At first employed in Paris in reorganising the navy, then in inspecting mainland France's ports, in 1801 he was put back into active service, at first on the ship of the line Océan, then on the Mont Blanc, the latter of which was part of the naval force under admiral Villaret for the Saint-Domingue expedition.

He joined Villeneuve in the Antilles and commanded the rearguard in the Battle of Cape Finisterre (July 1805) against admiral Robert Calder's squadron.