She later allegedly joined the Filiki Etaireia secret society which sought to achieve Greek independence from the Ottoman Empire, being among the few women to do so.

Following the outbreak of the Greek War of Independence she commanded a fleet of Spetsiot ships which contributed to several campaigns most notably the siege of Nafplion.

Lazarou had previously double-barrelled his family name to Lazarou-Orlov in order to commemorate his participation in the Orlov revolt and declare his loyalty to Russia.

Her stepfather encouraged her interest in sailing beyond the accepted social norms of the time, a decision which has been attributed to his admiration for Russian empress Catherine the Great.

On 10 April, the besieged Ottomans exploited the fact that the Greek sentries were celebrating Orthodox Easter, breaking through the siege.

In Argos, Bouboulina participated in a conference of local military commanders and kodjabashis, where the Greeks decided to resume the siege of Nafplion.

According to Dutch consul Taitbout de Marigny [tr; uk] she personally executed three Ottoman prisoners during her son's funeral ceremony.

The Ottomans were on the brink of surrender and were requesting a safe exit of the local officials along with their harems and release of a number of prisoners.

Bouboulina took an active part in the negotiations, intervening to save the lives of the women from Hursit's harem upon Valide Sultan's request.

Bouboulina was subsequently accused on taking part in the looting (which was a common practice in both Greek and Ottoman warfare of the period).

[20] On 3 December 1822, the Ottoman population of Nafplion was allowed to safely depart for Asia Minor, surrendering the city to the Greeks.

[20] Bouboulina was appointed to one of the commissions tasked with redistributing the property of Nafplio's Muslim population, a position she abused for personal gain.

[22] She and Panos Kolokotronis were blockaded in the city by pro-governmental forces from 8/20 March 1824, at sea by Miaoulis with two brigs and two gunboats, and on the land by 500 Kranidiots and Poriots.

[23] After the agreement that put an end to the first civil war, P. Kolokotronis eventually surrendered the fortress on June 7/19 and joined his father in Karytaina[24] Discussions about Bouboulina's treatment illustrated the growing dissent between members of the victorious governmental faction: the president Koundouriotis insisted on her expulsion from Nafplion, while Zaimis and Londos interceded in her favor, to no avail.

Although Theodoros Kolokotronis wanted to giver her in marriage to someone of his choice, Bouboulina secretly took her daughter Eleni back, leaving her dowry behind, perhaps to marry her to the Northern chieftain Theodore Grivas in order to secure an alliance with him, or because the two had alteady an extramarital affair[27] After the final defeat of his faction in the second civil war, Kolokotronis was imprisoned in February 1825.

A bust of Bouboulina created by Lazaros Lameras is located in Tinos while a copy of it hosted in the Pedion tou Areos.

[35] The Greek drama film, Bouboulina, starring Irene Papas in the titular role was released in 1959, it was directed and written by Kostas Andritsos.

[37] Lela Karagianni (sometimes spelled Karayanni or Carayannis), leader of the Greek Resistance cell Bouboulina during the Second World War, was her great-granddaughter.