In the years of 1922 and 1923, after the World War I, only some of the windows in the church were replaced, the cloister fell into disrepair. World War II and the following years meant a complete absence of repairs and maintenance of the entire area.

In 1953, the government became the owner of the pilgrimage site and took over the obligation to ensure its maintenance. However, the renovation of the building took place only in the 1970s and early 1980s.

Due to the development of the theory of the care of the historical monuments and its influence on everyday practice, the preparation of the renovation and the gradual processing of detailed surveys and creation of projects for individual reconstruction interventions took place. The search for an authentic form and the reconstruction works were not without professional errors in some respects and problems also began to appear in the sphere of the personnel providing the interventions. New generations of craftsmen lacked the knowledge and habits related to the usage of original technologies.

In 1994, the preparation of the documents for the application of the church to be included in the UNESCO World Heritage List began. At the end of 1994, the UNESCO World Heritage Committee approved the inclusion of the pilgrimage church on this prestigious list.

This undoubtedly significant event has further tightened the view of the professional institution, the National Heritage Institute, on all renovation events related to the church and the whole area. All steps in the reconstruction process must therefore not only be well considered, but also documented and presented in the so-called monitoring report, which is prepared every year for all monuments included in the World Heritage List.

In 2001, the pilgrimage church of St John of Nepomuk at Zelená hora was transferred from the administration of the District Office of the National Heritage Institute in Žďár nad Sázavou to the administration of the National Heritage Institute in Brno. Under this administration, the restoration of doors, floors, plaster repairs, repair of the roof and the interior dome, and an addition and restoration of stars took place.

Since 2008, the pilgrimage church has been under the administration of the Regional Office of the National Heritage Institute in Telč. Since January 1, 2013, the administration has been transferred to the Regional Office of the National Heritage Institute in České Budějovice.

In June 2013, the Diocese of Brno submitted an application for the release of the pilgrimage church as part of the so-called church restitutions. On August 27, 2014, representatives of the National Heritage Institute, the Roman Catholic Parish of Žďár nad Sázavou – II and the Diocese of Brno signed an agreement on the release of the property. Since August 28, 2014, the church has been under the administration of the Roman Catholic Parish in Žďár nad Sázavou – II.

Vladimír Záleský, the long-time parish priest of Žďár, managed to start general renovation of the entire area shortly afterwards. This has been going on since 2016 and included the restoration of plasters, the removal of previous inappropriate construction interventions, the overall renovation of pilgrims' area and also the installation of new elements in the cloister - a drinking fountain, a place of worship, the stations of the cross and benches.