The interior is covered with groin vaults on straps, flowing down to wall pillars bearing a prominent broken cornice. The rainbow arch is semicircular and has an ornately carved beam with a crucifixion group on a globe. It is late Baroque and dates from the 17th/18th century. The main altar is classicist from the 1840s. The church was built in the late 19th century.  On the curtain, there is a 15th-century Gothic sculpture of the Virgin and Child  and an 18th-century Baroque painting of St Joseph. In the antependium of the altar is an inset cordovan from the second quarter of the  18th century, brought back after the Battle of Vienna in 1683 by Hetman Stanisław Jabłonowski's soldiers. The two early Baroque altars are from 1618, while the other are from the 18th century, and the pulpit and the baptistery from the late 17th century. The statues of St Odile and St Jadwiga of Silesia are from 1470 and come from Wawel Cathedral.

Between 2020 and 2022, the church underwent a comprehensive conservation and restoration as part of the project 'Preserving and highlighting the multicultural heritage of the Muszyna area by carrying out repair, construction and conservation work on the baroque church in Muszyna', which was part of the 2014–2020 Regional Operational Programme of the Małopolskie Voivodeship.

The scope of the project included:

- roof renovation
- renovation of the facade and external threads
- renovation of the bell tower and chapel
- communication space around the church
- construction and conservation work inside the church
- conservation works – movable monuments, including:

1. conservation of the main altar
2. conservation of the north side altar of  St Joseph
3. conservation of the south side altar of  St John the Baptist
4. conservation of the side altar in the nave of  St Sebastian
5. conservation of the side altar in the nave of  the Sacred Heart of Jesus
6. restoration of the side altar in the nave of  Our Lady of the Rosary
7. conservation of the side altar in the nave of  Jesus Crucified
8. conservation of the side altar in the nave of  St Anthony of Padua
9. conservation of the rood beam with the Crucifixion group
10. conservation of the pulpit
11. conservation of the baptismal font
12. restoration of the following paintings: St.  Anna Samotrzec, Feast at Szymon's, portrait of Bishop of Kraków Andrzej Załuski, portrait of Bishop of Kraków Andrzej Trzebnicki.