He was constantly employed on missions in the provinces, and distinguished himself by his staunch repression of opponents of the anti-Revolution risings in the départements of Landes, Basses-Pyrénées and Gers. With his colleague Jacques Pinet (1754-1844) he established at Bayonne a revolutionary tribunal, with authority in the neighbouring towns. A local society denounced him for cruelty before the Convention in 1795, but charges were dismissed. He had represented the Convention in the Revolutionary Armies of Brest and of the Eastern Pyrenees in 1793, and in 1795 he was sent to the armies of the Moselle and the Rhine.
He managed to escape prosecution during the Thermidorian Reaction, assisted Paul Barras in resisting to the 13 Vendémiaire insurgency, and was a member of the Council of Five Hundred for a short while during the French Directory. Cavaignac filled various minor administrative offices under the Consulate and French Empire, and in 1806 became an official Joachim Murat's administration of the Kingdom of Naples. During the Hundred Days he was préfet of the Somme. At the Bourbon Restoration he was proscribed as a "regicide", and spent the last years of his life in Brussels, where he died.