Since the most valuable part of the monastery is its library, which is accessible only by special permission, its contents are presented in the Museum in a modern way so that visitors can still experience the treasures it holds. The library of the St. Francis Monastery is one of the five most valuable heritage libraries in Croatia, thanks to the Franciscans who have carefully preserved rare and valuable books for centuries, having been present in Šibenik since the 13th century. It houses a large number of incunabula, codices, parchments, and other rare and valuable books, most notably The Šibenik Prayer from the 14th century, one of the oldest Croatian linguistic and literary monuments written in the Latin script. The Museum also displays a rich collection of Gothic and Baroque reliquaries, as well as altarpieces and other paintings and artifacts. The monastery's musical tradition is presented in four categories: the organ, the Šibenik Prayer, choral chants, and the motets of Ivan Lukačić. You can explore and listen to each of these categories as part of the Museum's interactive exhibit.

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Since the Church of St. Francis is also the Croatian National Shrine of St. Nicholas Tavelić, a native of Šibenik and the first Croatian saint, one exhibit in the Museum holds a special place. These are the leather sandals of St. Nicholas Tavelić, which were sent to the St. Francis Monastery by the guardian of the Franciscan monastery in Jerusalem after his martyrdom in the Holy Land. You can also purchase "Nicholas's sandals" at the Museum – a commemorative souvenir in the form of a magnet or keychain – and take home a reminder of the first Croatian saint from Šibenik.

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The museum does not have set opening hours; visits must be arranged in advance by phone or email, so we recommend checking all information on the monastery's official website.