In addition to providing scientific advice and supervision in the extra-museum areas mentioned in the Functions and competences section (including the Basilicas and the Vatican and Lateran Apostolic Palaces), the Department directs the restoration of movable paintings and supervises the restoration sites within its competence, guiding interventions for the recovery and conservation of pictorial or architectural complexes of particular importance and media renown. These include the Sistine Chapel (completed between 1980 and 1999), the Niccoline Chapel (1995-96), the Pauline Chapel (2002-09), and the Gallery of Geographical Maps (2012-2016), as well as the Raphael Rooms (begun in 1982) and the Borgia Apartment (begun in 2006), both of the latter projects have been carried out over recent years and are now (November 2020) in their final stages.

Important and highly significant restorations were those of the frescoes in the Passionist complex of the Scala Santa (including the atrium, chapels and staircase itself), carried out between 2002 and 2020 by external workers under the joint guidance of the Museums' scientific and laboratory staff, and that of the ancient Oratory of St. Lawrence in Palatio (Sancta Sanctorum Lateranense), regarding the mosaics, the medieval paintings and the 16th century parts of the decoration, carried out under the same conditions by an external company (1992-1994).
Of additional note is the restoration of the venerated icon “of St. Luke” (Salus Populi Romani) of St. Mary Major Basilica, of ancient antiquity and beauty, freed from successive repaintings and restored to the faithful in conditions of renewed splendour and safety (2017).

Among the most recent projects tackled by the Department (November 2020) are those of Bramante's Courtyard of the Pinecone (started in 2014), the Hall of Constantine (started in 2015) and the Ducal Hall (started in 2018), all three in collaboration with the institutionally engaged museum and extra-museum institutions (Cabinet of Scientific Research Applied to Cultural Heritage – Vatican Museums; Painting and Wood Materials Restoration Laboratory – Vatican Museums; Superintendence of Architectural Heritage – Vatican Museums; the Directorate of Infrastructure and Services – Governorate S.C.V.). They are still in progress.

Recently, with the technical support of the Conservator's Office, new lighting and air conditioning systems have been installed in the Sistine Chapel (2014), followed by similar installations in the Raphael Rooms (2017) and in Room VIII (the so-called Raphael Hall) of the Pinacoteca (2020), in order to improve the conditions for visiting and appreciating the most well-known rooms.