These works were followed by a series of others which the town's priors commissioned from him on 21 st April 1466 for the Town Hall. Of these, a detached fresco of Christ on the Cross adored by Saints Jerome and Francis and the patron (probably the podesta of San Gimignano), preserved in the Museum of Sacred Art, still survives together with another, and another work of particular importance of its kind: indeed, Benozzo was entrusted with the restoration and completion of the Majesty painted by Lippo Memmi in 1317 in the Council Chamber, now known as the Sala di Dante (Dante Room). This fresco was considered one of the symbols of local civic glory and had already undergone alterations during the second half of the fourteenth century by a Sienese painter who extended the scene with the addition of two pairs of saints. On 16th December 1461, the Town Council passed a resolution for two doorways to be made, in the very section of the wall on which the fresco was painted, in order to link the Court Room with the adjacent Chancellery Room. In 1464, Benozzo was commissioned to restore the ruined parts of the original painting and replace certain missing elements. The work was not completed until 1467, as can be seen from the lower right-hand margin of the frame which reads "BENOZIUS FLORENTINUS PICTOR RESTAURAVIT ANNO DOMINI MCCCCLXVII". The artist's work consisted mainly of reapplying the names that had formerly accompanied the figures of the saints, repainting the faces of Barth and Louis of Toulouse, and the feet of John the Baptist. The artist also applied fresh gilding to the throne of the Virgin and repainted the sky with blue.

While mainly restorative in nature, these works played no small part in the artist's formative development, as demonstrated by the Virgin in Majesty with angels and saints which Benozzo began to fresco in the Council Chamber of Pistoia Town Hall but which remained at the sinopite (ochre pigment underpainting) stage due to the artist's premature death on 4th October 1497.