In September 1792, he was elected again to the National Convention as North MP. He joined the Mountain and was sent again on a mission to the Army of the North. The 26 December 1792, he requested a removal measure against the Interior MinisterRoland accused of destroying some of the evidence within the armoire de fer found in the Tuileries Palace, containing documents that indicated Louis XVI's relations with corrupt politicians. He demanded a roll-call vote for the trial of Louis XVI. He asked for death sentence without suspensions against the King. The day of the execution, he joined the Committee of General Security where he sat until June. He took advantage of his position to be resolutely opposed to Girondists and led an armed raid on the printing establishment of Antoine Joseph Gorsas on March 9, 1793. From 4 April to 20 July 1793, he was sent again on a mission to the North Army and he denounced the GirondistCharles Zachée Varlet but he supported suspected Generals as Custine and La Marlière against Jacobins as General Jean-Baptiste de Lavalette whom he dismissed. But Robespierre and Jean Bon Saint-André took the side of Lavalette and Duhem became himself somewhat suspect. The 12 December 1793, Robespierre delivered a speech supporting dismissed Mountain Generals. Duhem was excluded from the club 4 days later. To save his head, he was never heard again until 9-Thermidor.
Under the Thermidorian regime, Duhem belonged to the group of remaining Montagnards and went after Fréron and Tallien. Rather he stood up for Barère, Collot d'Herbois and Billaud-Varenne accused of terrorism. Close to the last sans-culottes, he was unable during the insurrection of 12 Germinal, Year III, to reconstruct the bands which in the past had insured the success of the journees. Arrested, he was imprisoned in Ham, then in Sedan but avoided trial. Released under the December 1795 amnesty, he joined the North Army as physician. Nevertheless, he remained politically involved and supported the main neo-jacobin movement during Directory as a member of the Panthéon Club. Dismissed in 1797, he was reinstated through the coup of 18 Fructidor. In 1798, he was accused of apologising for "the martyrs of the revolt of 1 Prairial Year III".
Late career
Transferred to the Italy Army, then to the West Army, he was posted to the military hospital in Mainz in 1802. Pierre Joseph Duhem died in Mainz in 1807 at the age of 48.