Napoleon and his troops reached Witebsk on July 28, 1812. There he stopped his army, because he had realized that he had reached a point where the problems in providing all supply for troops would became impossible. The distance to the central depots in Poland and Prussia were too far. Already, the distance to the new established depot in Wilna was more than 300 km. Due to the bad road conditions he considered supplying during winter, but snowstorms made this almost impossible and therefore he saw only two possibilities: either retreat to a better supply line or march forward to better areas between Smolensk and Moscow.

Initially the Russians employed a hit and run tactic, an excellent task for the Cossaks with their fast horses, and Napoleon therefore devised the Smolensk Manoeuvre in an attempt to sweep behind the enemy to win the battle. On August 14, troops of the French Central forces crossed the River Dnieper at Rassna using bridges constructed overnight. The plan was to race toward the city, taking it without a fight, and march north to attack the rear of the main Russian forces under the command of General Barclay de Tolly. Unfortunately for the French forces, conflicting orders and a breakdown in communication had already led Bagration to disobey orders and instead of marching west, he occupied Smolensk to the south. By August 16, French forces found the city heavily garrisoned by Bagration's troops, further reinforced with the arrival of the main Russian army. On August 16–18 it finally came to first major battle, the Battle of Smolensk between 175,000 men of the Grande Armee under Napoleon and 130,000 Russians under Barclay de Tolly, only about 50,000 and 60,000 respectively were actually engaged in the battle. The town was occupied by troops of the Russian corps of General Bagration and the French forces captured two of the suburbs but failed to bring the Russians out of the town.

Napoleon ordered an assault of three corps, supported by two hundred guns and artillery pieces. This was initially successful. The intensive artillery bombardment set the city on fire but the French forces did not have any ladders or other technical means to scale the walls and were under heavy counter fire from the Russian artillery. By nightfall, most of the city was burning and to save the army General Barclay de Tolly abandoned the city destroying all ammunition stores and bridges, leaving a small force to hold out for two days to cover his retreat during the night. The figures of casualties caused by the battle vary between 4,200 of French losses and 4,000-6,000 Russian men. Russians put their losses at around 6,000 whilst others state the French losses of more than 10,000 and Russian up to 12,000-14,000 men.

At the same time, the main Russian army was retreating for more than three months and making General Barclay de Tolly unpopular. The Tsar gave Barclay’s command to Mikhail Kutuzov. Against his own words Kutuzov continued in much the way Barclay had, immediately seeing that to face the French in open battle would be to sacrifice his army pointlessly. Following the battle of Smolensk on August 16/18 and after two stops he finally managed to establish a defensive position at Bordino near Moscow. On the same days, August 16–18, the right wing of the Russian Army, under the command of General Wittgenstein stopped a part of the French Army under Marshal Oudinot in the Battle of Polotsk. The Russian victory prevented the French marching on St. Petersburg, the Russian capital. This forced the French to concentrate on Moscow, where Napoleon himself led his forces.

The battle of Borodino on September 7 was the largest and bloodiest battle during the French invasion of Russia involving more than 250,000 troops and resulting in at least 70,000 casualties. The Grande Armee attacked the Russian Army under General Kutuzov near the village of Borodino, west of the town of Mozhaaysk and the Grande Armee captured the main positions on the battlefield but failed to destroy the Russian army. About a third of Napoleon's soldiers were killed or wounded. The Russian losses were much heavier, but could be replaced due to close proximity of the Russian training areas. The battle ended with a disorganized Russian Army. The state of exhaustion of the French forces and the lack of recognition of the state of the Russian Army led Napoleon to remain on the battlefield with his army instead of the forced pursuit that had marked other campaigns. The complete Guard was still available and in refusing to use it Napoleon lost this chance to destroy the Russian army.

The battle at Borodino was a turning point in the campaign, because it was the last offensive fought by Napoleon in Russia. By withdrawing, the Russian army kept its combat strength, and let the chance open to force Napoleon and his army out of the country. But after the battle the Russian army could only muster half of its strength on September 8, and was forced to retreat, leaving the road to Moscow open. Kutuzov also ordered the evacuation of the city. By this point the Russians had managed to draft large numbers of reinforcements into the army bringing total Russian land forces to their peak strength in 1812 of 904,000 with perhaps 100,000 in the vicinity of Moscow — the remnants of Kutuzov's army from Borodino partially reinforced.

The war was not yet at its end and both Armies continued their march. The Russian retreated for two reasons: first, their move was to the south and not the east and second the Russians began some operations that would continue to deplete the French forces. The rear guard on September 8 gave a strong resistance that Napoleon remained on the Borodino field. On September 9th, Miloradovitch assumed command of the rear guard adding his forces to the formation. Another battle throwing back French forces at Semolino causing 2,000 losses on both sides. The French Army started their move from the battlefield on September 10 while Napoleon, who was apparently sick (details are not known), did not leave until September 12. Some 18,000 men were ordered in from Smolensk, and Marshal Victor's corps supplied another 25,000. Miloradovitch continued his rear guard duties until the 14th allowing much of Moscow to be deserted. On September 14, 1812, Napoleon moved into the empty City of Moscow that was stripped of all supplies. Hoping on "the standard rules of warfare" when capturing an enemy capital Napoleon had expected a letter from the Tsar with an offer of his capitulation, but the Russian command did not think of surrendering. By that time the Grande Armee was already drastically reduced due to the large numbers of killed and wounded soldiers in action coupled with diseases (principally typhus), desertion of a large amount of soldiers, and long communication lines.

As Napoleon prepared to enter Moscow he was surprised to have received no delegation from the city. Normally, when a "victorious general" is approaching a city, the civil authorities present themselves at the gates of the city with their keys in an attempt to safeguard the population and their property. As nobody received Napoleon he sent his aides into the city, looking for officials with whom the arrangements for the occupation could be made. As nobody could be found, it became clear that the Russians had left Moscow unconditionally. In a normal surrender, the city officials would be forced to find billets and make arrangements for the feeding of the soldiers, but the situation caused a free-for-all in which every man was forced to find lodgings and other things for himself. Napoleon was very disappointed by the lack of "custom." Before the order was received to evacuate Moscow, the city had a population of approximately 270,000 people, as much of the population pulled out, the remainder burned and looted the remaining food to deprive the French of their use. When Napoleon entered the Kremlin he found one-third of the foreign traders and servants, all people who were unable to flee. These included several hundred members of the French colony attempting to avoid the troops.

After entering Moscow, the Grande Armée, unhappy with their military conditions and no sign of victory, started looting what little remained within the city. The same evening, the first fires began to break out, spreading and reemerging over the next few days. Moscow, comprised of mostly wooden buildings at the time, burnt down almost completely, depriving the French of shelter in the city. Observers claimed that the fire was not deliberately set, either by the Russians or the French; the natural result of placing a wooden city in the hands of strangers in wintertime is that they will make small fires to stay warm, to cook their food and for any other benign purposes and that some of the fires will get out of control. Without a fire department, house fires spread to become neighborhood fires and ultimately a citywide conflagration. The army spent just about one month in Moscow, but was ultimately forced to march back westwards. Assailed by the coming winter, starvation and disease, and permanent attacks by the Cossaks, the retreat destroyed the Grande Armée as a fighting force. Only 120,000 men survived to leave Russia and more than 50,000 of them were Austrians, Prussians, other Germans and other smaller nations, 20,000 Poles and 35,000 Frenchmen. And more as 400,000 died in the campaign.