In the presbytery is a ciborium raised on four gray-violet columns over the shrine of Clement in the crypt below.

The standard type of basilica was meant to hold a congregation of between 800 and 1400. It consists of a nave flanked by aisles and terminating in a semicircular, sometimes rectangular, apse; a narthex and atrium sometimes feature at the west end. This standard type of basilica is known as early as the late 4th-century church of S Ambrogio at Milan. After ca. 380 examples of the type at Rome include S Clemente. The schola cantorum is a term applied to nave chancels in medieval Roman churches on the basis of a supposed association with the eponymous body of papal chanters. This association originates in the misinterpretation of a 16th-century description of S Clemente by Ugonio. The form of Early Christian nave chancels was not standardized. Those at S Clemente (6th century) were apparently narrow passageways constructed of low parapets held together by posts and so lightweight that they did not need foundations. Fontana remodelled the nave of the upper church of S Clemente during 1701-1715 and was also responsible for the building's façade. The two-storey front is surmounted by a heavy triangular pediment and relates well to the atrium, which Carlo Stefano also designed.