Geoffroy de Thoisy commanded a Burgundian flotilla organized by Philip III the Good, Duke of Burgundy (r. 1419-1467) in May 1441 at the request of the Knights Hospitaller to help defend Rhodes against the Mamluk Sultan of Egypt. The duke went in person to Sluis to see off his flotilla. Throughout 1442, de Thoisy’s force was based at Rhodes, harassing the Muslim shipping and coastline. Having refitted at Villefranche, it was again in action off the North African coast and Rhodes in 1444. When a second Mamluk fleet assailed the island, the Burgundians helped the Hospitallers lift the siege of the town of Rhodes, which had lasted for forty days.

Next, in response to a Byzantine appeal for help against the Ottoman advance, Philip instructed de Thoisy and his squadron to reinforce the four galleys under the command of by Waleran de Wavrin and to join Pope Eugene IVs planned Crusade. De Wavrin's four galleys sailed in July 1444 but failed to stop Murad II's Anatolian army from crossing the Bosphorus. De Thoisy joined de Wavrin's squadron at Constantinople, where the latter had gone to spend the winter. In the meantime, on 10 November 1444 the crusading army led by Wladyslaw III of Poland (Ulaszlo I as king of Hungary) and Janos Hunyadi had been severely defeated by the united Anatolian and Rumelian armies of Murad II on the plain before the Black Sea port of Varna. In the spring of 1445, de Wavrin sailed to the Danube to join the Hungarians in the continuing Crusade of Varna, while de Thoisy took his ships along the south coast of the Black Sea. He had been tasked with exploring the southern shores in an attempt to find out about possible survivors of the battle of Varna.

He engaged in piracy there, plundering both ships and coastal settlements (notably the Turkish castle at Ünye), covering the expenses for the re-equipment of his ships at Trebizond with five slave-women, worth in all 164 ducats. In Trebizond, de Thoisy found out that a large merchant ship belonging to "Christian schismatics" planned to call at nearby Vaty (Batumi). Although the Emperor of Trebizond, John IV Megas Komnenos, (whose first wife was Georgian) warned him that the people of Georgia were Christians, de Thoisy nonetheless sailed towards Batumi, claiming that his orders were to fight all schismatics who did not obey the Pope. However, some Greeks from Trebizond informed the Georgians who, when they saw de Thoisy's galley coming, took up arms and waited in ambush.

As soon as Thoisy landed at the port of Batumi, the ambushers attacked, killing many of his men and taking him captive. Those of de Thoisy's men who managed to escape fled to the Genoese port of Caffa (modern Feodosiya, Ukraine), where they reported to de Wavrin. There, it was decided to ask the Emperor of Trebizond to secure de Thoisy's release. The captive knight's fleet, now reunited, thus sailed to Trebizond, where through the intermediary of the Genoese Girolamo di Negro, a member of the imperial court, de Thoisy was released in exchange for a guarantee that he would no longer attack people in the region. He had spent the entire month of May in captivity.

De Thoisy and his small fleet then returned to Caffa. On their way, they captured 400 Tartars as well as a small Turkish vessel from Ginopolis [Inebolu], whose cargo belonged to the pope Manuel of Soldaia [Sudak] in Crimea and included goods belonging to "Emin", a Greek. The Genoese authorities in Caffa ordered de Thoisy to sell his captives in order to compensate the latter, and his piracy also led to a protest from the government of Genoa to the Duke of Burgundy. Recalled to Constantinople, he was invited by de Wavrin to join a forthcoming expedition with the Hungarians and Vlachs, but de Thoisy preferred to return with his ships to France.