The Earl of the Grand Duchy of Lithuania, Count Jonas Karol Chodkevičius, with his wife Sofia, sought to distract the population from paganism and protect it from the spread of Prussian Protestantism. He built the first wooden church in Kretinga and established St. Franciscan Monastery of the Minor Brothers, also known as the Bernardine. Seeing the great success of the monks’ work, the Earl next year ordered the preparation of the material for the new monastery building. The construction started in 1605. In the 19th century a new stone church was built with the most famous organ throughout Samogitia. For the construction of a brick monastery and a church, Chodkevich dedicated the 12-year income of Kretinga manor. The monks themselves built a mill on the Pastauninko stream.

The monastery was robbed and devastated by the Swedish army in 1659 and 1710.  Not only did the Sapiegos repair the buildings, but they also renovated the great altar. It is believed that sculptor and painter Jokimas Dobročinskis contributed to the interior decoration of the church. Many monks died during the Great Samogitian plague. They were rescued from hunger by the owners of the mansion, who sent them bread.

The Kretinga monastery was classified as permanent, but did not allow the reception of the Novices, and sent to it the priests and the people of the closed monasteries who had committed most of the tsar’s rule. 1886 After the closure of the Kęstaičiai Rococo Monastery, which also housed a priestly refuge, its inhabitants with mental disorders were relocated to Kretinga. There were also priests (mostly drunkards) who had broken their spiritual discipline.

The revival of the monastery is connected with the priest Antanas Bizauskas. He joined the monks in 1912, with the permission of the authorities, choosing the name of Francis. The monastery in particular flourished and had aroung 110 people during the interwar years in Independent Lithuania. A modern school, St. Anthony Mission College and St. Anthony’s Palace was built. It had its own printing press, bookbinder, movie theater.

In 1940, the Bolshevik monastery closed, some monks were deported, and the Red Army was inhabited in the building. In 1941 a fire broke out in the city, severely destroying the church and monastery buildings. The Franciscans who returned during the German occupation tried to revive their activities, but the second Soviet occupation prevented them from doing so. 1946 again the monastery and school were closed, the Kretinga church pulpit was exiled to Siberia and the others scattered. 1949 registration of the Kretinga monastery church was not allowed and all property was confiscated beforehand. Soldiers lived on the premises of the monastery and were later transferred to the Museum of Regional Studies, which restored them. The Franciscans held the first Mass in their former shrine in 1989. This date is considered a celebration of the Franciscan return to Kretinga. 1991 the monastery’s premises were returned to them.

The monastery did not lose its ensemble. The following buildings are preserved: the Blessed Blessed Virgin Mary. Church of Our Lady, Monastery, School, St. Anthony Institute, power plant, workshops, shepherd’s house, teacher house, grotto – Lourdes, workshops, laundry, outbuilding and stone house in the churchyard, which may have been used as a shed.