In French service, Eickemeyer was employed first in the Taunus region, where his local knowledge was useful in the maneuvers along the Nahe. After the defeats suffered there by the French, he retreated behind the Queich tributary with the rest of the French Army. He transferred to the Upper Rhine, promoted to brigadier general, and spent a short time in the previously Swiss territories. In the Fall 1793, he went to the French town of Belfort, where he evaluated the defenses and trained troops. In 1795, he was assigned to the besieging army at Mainz, and there he used his free time to write a short history on the capture of the fortress of Mainz by the French troops in 1792, which was printed two years later. In 1796, he belonged to the Army of the Rhine and Moselle, under Jean Victor Marie Moreau's command, and in the retreat across Germany he commanded the rear guard, which had several serious clashes with the Austrians. For most of 1796, he fought in the first division of Louis Desaix's Center, under the command of Delmas.