The painting is in very poor condition, having been transferred from its original panel to canvas. This canvas has then been lined onto another canvas. Still on its original panel in 1729, the painting was described in 1786 as being on canvas. The Mackintosh Madonna can possibly be identified with a Madonna by Raphael from the Orléans collection that was transferred by the restorer Robert Picault in 1751. He used a highly dangerous technique to separate the paint from the panel. He kept his method ‘secret’ but it seems that he destroyed the ground layer (between the paint and the panel) through prolonged exposure to nitric acid vapours. This allowed him to display intact the original wooden support alongside the transferred painting.

Although the Mackintosh Madonna was already described as damaged when first recorded in the eighteenth century, its ruinous condition can mainly be attributed to the transfer. Large areas of original paint are missing, including an area down the centre of the panel (which may be related to early problems with the original wood panel), and the surviving paint is much abraded and covered with restoration and very discoloured varnish. The paint surface now has the texture of a canvas painting. A triangular area of paint, comprising the proper left side of the Virgin’s head, her shoulder and part of the sky may have become completely detached in the transfer process, which might support the supposition that Picault was responsible. A strip along the left edge, including the tower from which the painting takes one of its names, seems to have been added in the eighteenth-century.

Since its presentation to the National Gallery in 1906, the painting has received only minor treatments, mainly the securing of loose paint and a surface cleaning and revarnishing in 1928.