Records of the existence of a Franciscan monastery in Osijek in the pre-Turkish period are not historically confirmed. Although there are traditional stories of Franciscans in the nearby village Anitno, there are no existing proofs of any Franciscan monastery on that locality to this day. After Turkish defeat in Vienna 1683, and the victory of the Christian army at Nagy Harsany on 18 August, 1687, Slavonia was liberated, and so was Osijek, where the Franciscans instantly took up residence.
They settled and remained to this day in the oldest part of the town, Tvrđa. In the first ten years their living conditions were very poor. They had one poor apartment which P. Simon from Vienna moved into back in 1687. They had no finances to build a bigger monastery, while up to 1692 the area wasn't perfectly safe. In 1699, thanks to endeavours of P. Pavle from Rama, the Franciscans took up building the original monastery with two wings – eastern and southern – in the shape of the letter "L". The construction works lasted till 1705. A year later the monastery was officially founded. Guardian P. Petar Osječanin enlarged it, and P. Martin Osječanin built two more storeys.

1733 the Franciscans started building a new monastery on a piece of ground south of Klanac, which they were given as a gift by the War Chamber. After some difficulties, construction works were continued 1752 – 1757. The building was completed 1761. The new monastery is connected by vaulted arches with the east wing of the old monastery building, and by an added hall with a staircase along the north wall of the church, which leads to the then built choir.
The Franciscans had to give this monastery over to military authorities to serve as armoury on 16 June 1786, and move into Jesuit residence next to the parish church of Michael the Archangel on the Jesuit Square (today Juraj Križanić Square). Into their present premises the Franciscans moved 1938 after the exchange of the Jesuit residence for the building of the then State Ministry of Defence in the Franciscan Street (today Vatroslav Lisinski Square).

The monastery and the Franciscan church, monuments of the highest cultural and religious value, together with the rest of this historical part of Osijek, Tvrđa, were considerably damaged during the Homeland War 1991/1992 by several direct missile hits. Monastery roof was completely ruined, in several rooms ceilings collapsed, and church windows shattered. Shrapnel damaged the church facade and partly the interior and its inventory. Due to massive devastation the full restoration of the facade and the interior church walls has not yet been finished, in the first decade of the 21st century.