At about 6am on 14 June 1800, the Austrian army began to slowly emerge from its bridgehead on the east bank of the Bormida river. Because it was such a cramped position, the Austrian deployment was time-consuming. As they deployed, elements of Melas's centre started attacking Gardanne's division, deployed ahead of the stream, from about 7 o'clock.

By 10am the French had deployed sufficiently to allow for Victor to order Gardanne to retreat back across the Fontanone. Chambarlhac's division was soon deployed to hold Marengo and Lannes with Watrin's division formed on its right flank. Around this time Napoleon realised that this was no diversionary attack and sent a frantic message to Desaix, recalling him and Boudet's division, and marched toward the battlefield. By 11 am Bonaparte was on the field and summoned up his last reserves. Jean-Charles Monnier's division and the Consular Guard were ordered to extend and shore up the French right, under pressure from Feldmarschall-Leutnant Ott's two divisions, rather than to try to hold Marengo.

While an Austrian attack on the French left at noon was unsuccessful, by this time Ott had started to turn the French right. At 2pm, with their men exhausted after beating back several major Austrian assaults and running dangerously short of ammunition short, Victor and Lannes finally abandoned Marengo and the line of Fontanone Creek. The French fell back slowly, and in relatively good order, harassed by cavalry and pounded by artillery. Monnier's division and the Consular Guard arrived and were committed to stop Ott's advance, but they were also forced to retreat. Meanwhile Desaix, apparently already en route, having marched to the sound of the guns, met Napoleon's staff officer on the road.