The altarpiece has undergone numerous alterations. Shortly after its arrival from Antwerp, a figure of St. Michael was placed on the upper section. The figure was removed again, however, in the XX century. During the Spanish War of Independence, the altarpiece was dismantled and later re-assembled, which was probably when its protective wings and several figures were lost, all of which makes the iconographic identification of any particular scenario particularly difficult. In 1846, the sculptor of religious figures, Pedro de Valdivieso, replaced two missing heads: one in the scene of the Crucifixion and Presentation and the other which, regrettably, has not survived down to the present.
Different transformation processes have added assorted wooden elements, re-positioned pieces, cleaned, re-gilded and re-varnished the polychromy several times, albeit very discreetly. Figures were re-painted with polychrome decoration that was generally applied using many different assorted substances.
In 2013, the altarpiece was restored by CROMA under the guidance of the Alava County Council's Restoration Department.