When the Assembly adjourned, he became President of the Criminal Tribunal of the Department of Seine et Oise, and was sent as their representative to the National Convention in 1792.

Back in France he was made Receiver-General of the Department of Seine et Oise, but on the overthrow of the Directory on the 18th of Brumaire, he returned to the diplomatic service on behalf of the new Consulate.

When he was replaced in Madrid at the end of 1800 by Lucien Bonaparte, he was sent to Florence in February 1801, as Minister Plenipotentiary, to arrange peace with France.

At the end of 1805 he was transferred to Rome as a substitute for Cardinal Fesch, Napoleon's uncle, who had gone with Pope Pius VII to Paris.

With the fall of Napoleon Alquier was recalled, and with the return of the Monarchy under Louis XVIII, he was condemned to exile as a regicide.