Thrown into prison during the Reign of Terror, on an unsubstantiated charge of friendliness to the Royalists and the British, he was released after the fall of Maximilien Robespierre in the summer of 1794 (during the Thermidorian Reaction), and rose through the ranks until, in 1799, he became chief commissary to the French Revolutionary Army serving under André Masséna in the north of Switzerland.

He did not however limit himself to his tasks, and found time, even during the campaign, to translate part of Horace and to compose two poems, the Poème des Alpes and the Chant de guerre – the latter was a condemnation of the murder of the French envoys to the Second Congress of Rastatt.

The accession of Napoleon Bonaparte to power in November 1799 (the "18 Brumaire coup") led to the employment of Daru as chief commissary to the Army of Reserve intended for Northern Italy, and commanded nominally by Louis Alexandre Berthier, but really by the First Consul.

It was afterwards asserted that, on Napoleon's resolve to turn the army of Great Britain against the Habsburgs after the proclamation of the First French Empire, Daru had set down at the dictation all the details of the campaign which culminated in the battle of Ulm.

After this he supervised the administrative and financial duties in connection with the French army which occupied the principal fortresses of Prussia, and was one of the chief agents through whom Napoleon pressed hard on that land.

In 1811 he became secretary of state in succession to Hugues-Bernard Maret, duc de Bassano, and showed his ability in the administration of the vast and complex affairs of the French Empire, including the arrangements connected with the civil list and the imperial domains.