The choir was manufactured in walnut and chestnut wood in 1598, during the reign of Grand Master Fra Martin Garzes at the expense of the Grand Prior of the Church Giorgio Giampieri. It is composed of an upper and lower tier and contains fifty-two pews with elaborately gilded carvings. The lectern was installed during the reign of Grand Master Cassiere (1572-1581). Both works have been attributed to Antonio Lazi a wood sculptor from Piacenza, Italy. The restoration process commenced with the cleaning of the choir stalls from several layers of darkened varnish, dirt and grime followed by the repair of losses in the gilt decorative scheme. Repairs were also carried out on the carvings. The stalls were also treated against biological and insect infestation. To finish the restoration process a layer of protective coating was applied.

Restoration of the choir stalls and lectern commenced in November 2013 on the initiative of The St John’s Co-Cathedral Foundation and completed in April 2014.