This section has an important role in the frame of the entire work of the institution. It is divided into several specialized sections depending on the material they work with and the essential goal of this section is to preserve the authentic appearance of the museum and other items, through undertaking certain preventive, conservation-restoration, and technical activities.
In the first place, investigations are undertaken, followed by the preparation of the findings, identification and registration, and preparation of the complete required documentation.
The most significant projects are:
- Conservation of the painted surfaces of the Hamza Bay Mosque
- Conservation of the fresco paintings of the church of St. Dimitire Bitola
- Preventive protection of the mosaic surfaces of the locality of Heraclea Lyncestis
- Conservation of the restoration of the church of St. Petka in the village of Malovista
- Conservation of the icons of the church of St. Bogorodica Bitola
- Conservation and restoration of the numerous movable items of ceramics, textile, metal, wood, etc. from the collections o the Bitola Museum.
- Conservation and restoration of the decorative wall paintings of the interior of the Bitola house from the beginning of the XX c.

- Conservation and restoration of the frescos of the church Uspenie na St. Bogorodica v. Velusina
- Conservation and restoration of the fresco painting of the church Arhangel Mihail v. Sredno Egri
- Conservation and restoration of the fresco painting of the church St. Bogorodica in v. Graesnica
- Conservation and restoration of the fresco painting of the church of St. Dimitrie v. Gradesnica
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