At the resumption of activities, the panel was taken to the laboratory, where the restoration and consolidation project was initiated, which included the following operations

• Reconnaissance and study of the support structure and evaluation of the functionality of the wood movement containment system
• Consolidation of the pictorial film
• Aesthetic revision of the pictorial surface: removal of greasy dust deposits, plastering, and pictorial reintegration of the consolidated and repaired areas
• Revision of the final varnishing of the entire painted surface
• Modification of the support structure to restore the functionality of the system
• Transportation and relocation of the work to its place of origin

The first operation carried out on arrival at the Vatican was the partial removal of the support structure, which couldn't control the movement of the wood, underlying the conservation problems of the pictorial layers.

The panel, thus freed from the constraints of the metal structure, was left in storage for some time to allow the wooden support to settle, a period that extended beyond the original schedule due to the closure.

Between 2000 and 2001, following an initial emergency protection and veiling intervention carried out in 1994, the painting was carefully restored in the Vatican Museums' Painting Restoration Laboratory by restorers Giovanni Cecchini, Javier Camacho Barbasan, Marcello Mattarocci, and Massimo Alesi.

The main problem found in the painting was the presence of severe lifts and gaps formed due to the lack of adhesion between the preparation layer and the wooden support. The primary cause of this state of preservation was the poor quality of the wood used to make the panel. The restorers performed an in-depth study of the movements of the support, which led, at the same time as the consolidation operations of the pictorial film, to the design and construction of a metal structure to control the movements of the support.

After almost twenty years, an examination of the painting in 2019 revealed problems comparable to those discussed in the last restoration. A grazing light view showed the presence of very pronounced "curtain" type lifts.

Most of these were concentrated on the Virgin's mantle and along the left edge of the painting. A comparison with the graphic documentation of the state of preservation before the 2000 restoration showed that some of the lifts were contiguous with and corresponding to the areas where previous restoration had been done. In contrast, the lifts in the upper part of the right and left angles and the line between the landscape and the sky were in areas that had not previously manifested degradation.

The work was also affected by altered retouches with thick accumulations of greasy dust.

Before moving it to the Vatican Museums' Painting and Wood Restoration Laboratory and with the painting still on the wall, the restorers protected the areas affected by the detachments with an emergency veiling with Japanese paper and Klucel (5%) to secure the unstable areas of the painting and prevent any loss of the paint film. After injecting the consolidant, the restorers lowered the lifts by exerting light pressure with a double-leaf spatula, interposing a sheet of Melinex. To ensure proper adhesion of the paint film lifts and restore the original flatness, during the adhesive drying phase, the treated areas were left under the action of localized weights, again interposing a sheet of Melinex.