Despite the promise of reforms and quick recruitment of new forces, the strategic situation of the Polish forces was still critical. On 10 May the forces of Prussia crossed the Polish borders and joined the Russian armies operating in northern Poland. On 6 June Kościuszko was defeated in the Battle of Szczekociny by a joint Russo-Prussian force and on 8 June General Józef Zajączek was defeated in the Battle of Chełm. Polish forces withdrew towards Warsaw and started to fortify the city. On 15 June the Prussian army captured Kraków unopposed, but the Russian forces were defeated in a series of skirmishes near Warsaw and the defenders managed to finish the fortification efforts. Although it was besieged by Russo-Prussian forces on 22 July, the siege was unsuccessful. On 20 August, an uprising in Greater Poland started and the Prussians were forced to withdraw their forces from Warsaw. The siege was lifted soon afterwards, on 5 September. Russian forces commanded by Ivan Fersen were withdrawn towards the Pilica River.
Although the opposition in Lithuania was crushed by Russian forces (Vilnius was besieged and capitulated on 12 August), the uprising in Greater Poland achieved some success. A Polish corps under Jan Henryk Dąbrowski captured Bydgoszcz (2 October) and entered Pomerania almost unopposed. Thanks to the mobility of his forces, General Dąbrowski evaded being encircled by a much less mobile Prussian army and disrupted the Prussian lines, forcing the Prussians to withdraw most of their forces from central Poland.
Meanwhile, the Russians equipped a new corps commanded by General Aleksandr Suvorov and ordered it to join up with the corps under Ivan Fersen near Warsaw. After the battles of Krupczyce (17 September) and Terespol (19 September), the new army started its march towards the Polish capital. To prevent both Russian armies from joining up, Kościuszko mobilised his forces in Warsaw and on 10 October started the Battle of Maciejowice. Despite Kościuszko's plans, both Russian units entered the combat simultaneously and won the battle. Kościuszko himself was wounded in the battle and was captured by the Russians, who sent him to Saint Petersburg.
The new commander of the uprising, Tomasz Wawrzecki, was not able to control the spreading internal struggles for power and ultimately became only the commander of weakened military forces, while the political power was held by General Józef Zajączek, who in turn had to struggle with both the leftist liberal Polish Jacobins and the rightist and monarchical nobility.
On 4 November the joint Russian forces started an all-out assault on Praga, the right-bank suburb of Warsaw. After 4 hours of long hand-to-hand struggle, the 24,000 men strong Russian forces broke through the Polish defences and started to loot and burn the borough. The whole district was completely destroyed and approximately 20,000 of its inhabitants were murdered. The event became known as the massacre of Praga. Dispirited Wawrzecki decided to withdraw his remaining forces southwards and on 5 November Warsaw was captured.
On 16 November, near Radoszyce, Wawrzecki surrendered. This marked the end of the uprising. The power of Poland was broken and the following year the third partition of Poland happened, after which Austria, Russia and Prussia annexed the remainder of the country.