While the Silesian Army crossed the Rhine, the Austrian units on the left wing of the Bohemian Army continued the invasion of Franche-Comté. Marching south on the road to Pontarlier, Bubna's advance guard made contact with the French on 1 January at l'Hôpital-du-Grosbois, less than ten miles east of Besançon. On the same day, Bianchi's and Crenneville's divisions marched into Montbéliard, forty miles northeast of Besançon. After reaching Porrentruy on the 31st, Gyulay's III Corps entered French territory on New Year's Day at Delle, halfway between Belfort and Porrentruy. He posted his advance guard brigade at Blamont, while a second brigade received a double charge: support Wöber's Streifkorps after its check at Baume-les-Dames and take possession of the bridges over the Doubs at Clerval and Pont-de-Roide. Liechtenstein's II Corps likewise crossed into Franche-Comté, halting at Morteau, forty miles south of Gyulay's position at Delle. Filling the gap between III and II Corps, Colloredo's I Corps moved to Porrentruy on the 2nd.

On New Year's Day, Schwarzenberg assigned command of the II Corps and Moritz Liechtenstein's 2nd Light Division to Prince Friedrich of Hesse-Homburg, who received orders to besiege Besançon by 9 January with these units as well as his own Austrian Reserve Corps. With such massive Allied forces approaching, Prefect Jean-Antoine-Joseph de Bry of the Doubs Department found Besançon's garrison composed only of newly arrived conscripts and poorly mounted cavalry hardly capable of resistance.