In 1799 the Pavillon de Breteuil was occupied by a detachment of the army and was left in a sorry state. In 1799 citizen Maréchaux, architect of the Château, sent the following report to the Minister of the Interior: "... they have entirely destroyed the wood panelling and partly burnt the floor boards for heating and have removed the locks so that there are substantial repairs to be made..." Nevertheless, Maréchaux proposed letting the Pavillon on condition that the tenant carry out the necessary repairs. In 1802, soon after his installation in the newly restored Château de Saint-Cloud, the First Consul gave orders that the Pavillon de Breteuil should also be restored. It had been renamed Pavillon d'Italie as Napoléon had wanted to give it to Marescalchi, the Italian Foreign Minister. The building then took the external form it has today, the corners of the octogonal sections at each end becoming rounded (the present day 'Grande Salle' and salon of the Director's apartment) and the centre of the Pavillon being raised by a new upper section.

By 1806, although the main building was not yet finished, the outbuildings were being used as lodgings for twenty-four of the Emperor's horses, various members of his retenue and two park keepers. In the same year, work was carried out at the request of the Empress Joséphine to install a bathroom in the Pavillon for her to bathe in 'Barèges water', a sulphurous water whose vapours might, it was feared, damage the gilt in the Château.

In 1807 the apartments of the Pavillon d'Italie were finished and made ready for the arrival, in August of that year, of Jérôme, King of Westphalia and the youngest of Napoléon's brothers, who had just married Catherine de Würtenberg.

In March 1810 the Pavillon d'Italie was made ready for the Emperor himself to spend a night there. The intention was that this visit should take place while the Archiduchesse Marie-Louise stayed at Saint-Cloud, on the eve of her civil marriage to the Emperor. It seems that, at the last moment, Napoléon decided against the plan. In the same year the Pavillon d'Italie served as the residence of Caroline Murat, Queen of Naples and in 1811 the Princes of Holland [Napoléon-Louis and Charles-Louis Napoléon Bonaparte (later Napoléon III)], sons of Louis Bonaparte, stayed there. According to contemporary reports, the Emperor furnished the Pavillon with much taste and magnificence.

The Austrian occupation of 1814 seems not to have left any scars at the Pavillon de Breteuil. As soon as the Comte d'Artois moved into the Château de Saint-Cloud in July 1814, the architect Le Père was ordered to arrange the necessary rooms in the Pavillon de Breteuil so that the Prince could take showers there. The following year allied troops siezed the Pavillon. In marked contrast to the earlier Austrian occupation some, in particular those of General Blücher, did a great deal of damage. On 23 November, Le Père took advantage of the departure of the troops and removed the mirrors that had survived the pillage to the Château de Saint-Cloud for safety.