In May 1799, Klein led a cavalry division of 2,010 prior to the Battle of Winterthur. A few days later, he commanded the cavalry reserve against the Archduke Charles and the Austrian army at the First Battle of Zurich. Charles' superior numbers and position forced the French to retreat from Zurich, taking up position on the western side of the Limmat River. In September, he again commanded the cavalry reserve, the VII. Division, of 3,696 on the left (west) bank of the Aar river. He was responsible for guarding the Frick valley (Fricktal). There, as the dispositions developed for the Second Battle of Zurich on 25 September, Klein remained under direct command of Massena. Klein prepared to support either the troops of Jean Thomas Guillaume Lorge or Édouard Adolphe Casimir Joseph Mortier, on the north or south flanks respectively, as required. The Austrian assault fell hardest on Mortier, who was driven back from the strategically placed Dietikon. Klein's reserve enabled the French to retake and hold the village. This convinced the Russian commander in Zurich, Alexander Korsakov, that he should draw his troops back to the city fortifications. Later, as Korsakoff relinquished these, the Russians executed a confused withdrawal to Constance. In the chaos, Honoré Théodore Maxime Gazan's division, supported by Klein's reserve, pressed the Coalition forces hard at the west end of Constance, by the bridge to the abbey at Petershausen. They nearly captured the Prince Condé and the Duke d'Enghien themselves. Although the French took many prisoners, including many of the Army of Condé, the French emigrant army, these prisoners were not massacred whole-sale, as had happened after earlier battles. Klein and Mortier issued instructions, which were supported by Massena, that the émigrés be assigned Russian names—they were, after all, under Russian pay and wearing the Russian cockade in their caps—and treated with dignity; they were eventually exchanged for French officers held prisoner by the Austrians and Russians.