By 1800, he took over from his father, Nikolos, as leader of the local armed band of armatoloi. As such, he took part in negotiations with other leaders ("Kapetanei") and made the acquaintance of Ioannis Kapodistrias.
Early in 1821, Varnakiotis was assigned the task of declaring western Roumeli in revolt against the Ottoman Empire. He did so on May 25 of that year - two full months after the rest of Roumeli and the Peloponnese - most likely due to caution on his part. He then took part in the siege of Vrahori (Agrinio) which fell on June 11.
In 1822, he took part in the Battle of Komboti and the Battle of Peta. The latter proved a costly defeat which allowed the Ottoman army, under Kutahye, to advance towards the south. Varnakiotis and his men took up positions on the hill of the Prophet Elias near Aetos and engaged the Turks. The battle which ensued ended in victory for the Greeks on August 10, averting a complete disaster for the Revolt in western Roumeli.
In October 1822, Varnakiotis was replaced by Markos Botsaris as leader of the Greek revolutionaries in western Roumeli. This was due to accusations of treason and cooperation with the enemy - charges which he denied. He fled to the Ionian Islands where he stayed until 1827. At that time, he was reinstated by the leadership of the war effort and he took part in the last battles of the war.
After Greek independence, he was promoted to "chiliarch" by Governor Ioannis Kapodistrias. In 1830, he was appointed Judge of the Military Court of western Roumeli and, in 1836, he was made Lt Colonel by King Otto.