The church had to be furnished for its consecration, which took place on September 27, 1722. On this occasion, the furnishings were mostly temporary and they were later replaced by permanent pieces. The altarpiece, as the central and most important part of the church, was designed by Santini himself.

The background of the altar is formed by a richly decorated and pleated canopy on a cornice. The central statue represents St John of Nepomuk standing on a globe and rising upwards. The five eight-pointed Cistercian stars on the globe represent the 5 continents on which Christianity was spread. The globe is carried by three angels, compositionally arranged in the shape of the letter V, the other two equally large angels on the sides push the canopy aside forming the background of the entire scene. Above the saint's head there is another trio of small angels, one of whom holds a key in his hand and the other one a seal, which can be yet again understood as a reference to the saint's silence. The side altars are dedicated to four evangelists: St Matthew with an angel, St Mark with a lion, St Luke with a bull and St John with an eagle.

The work on the main and side altars was started by the sculptor Jan Pavel Czechpauer from Chrudim based on Santini's designs. After his death, the main altar was only completed in 1729 by the sculptor Řehoř Theny, whose work also includes the sculptural decoration of the pulpit. The silver pilgrimage statue of St John of Nepomuk was made according to Theny's model by the goldsmith Jan Norbert Diesbach from Prague.

The cloister around the church has the floorplan of a ten-pointed star and it can be entered by five gates. The roofs of the gates were originally decorated with five statues of St John of Nepomuk's virtues, three of which have survived to this day, and the statues were accompanied by shield bearers. There are also mentions of bells in the contemporary sources, of which there were also five. The original rich decoration of the cloister formed by stucco patterns and ribs on the vaults has been preserved only to a small extent. The cloister contains five chapels, one of which is decorated with frescoes. This chapel was called the German or Bavarian Chapel, because masses were celebrated in German there for pilgrims from German speaking regions. The cloister was designed by the architect at the same time as the church, but it was probably not completed until around 1735. This means that the architect Santini did not live to see the final completion of his work, as he died in 1723. The cloister, which is a typical feature of pilgrimage sites, had a practical purpose: It served pilgrims who came to Zelena Hora to let them hide from the rain and even rest and spend the night there. On festive occasions, the interior walls were decorated with a number of symbolic scenes placed in cartouches. The harsh winters of the 1760s were the reason for slight modifications to the cloister; some portals from the corridor to the courtyard were bricked up and the portals of the gates and chapels were lowered.