The 5th century figurative mosaic panels on the nave side walls are of first importance. There are now thirty-six panels left of the original forty-two, since six were lost when the Pauline and Sistine Chapels were built. Some of the thirty-six were heavily restored with paint during the Middle Ages, and some were reconstructed in fresco in 1593 and later. This is especially the case with those nearer the entrance. A total of nine mosaics on the thirty-six have been completely lost, leaving twenty-seven mosaics. The left hand cycle features scenes from the lives of the patriarchs Abraham, Isaac and Jacob. Twelve panels survive. Most of these each depict a story in two or three conjoined scenes. The right hand wall depicts The Journey to the Promised Land. Fifteen mosaic panels survive.

Above the nave side wall mosaics, on the blocked windows mostly, are a series of late Mannerist frescoes featuring scenes from the life of Our Lady. The set was commissioned by Cardinal Pinelli originally, and were mostly painted in 1593 (except for three).

In the reign of Pope Eugene III (1145-53), the extant exquisitely intricate Cosmatesque floor in the central nave was laid. This pavement was restored in 1593 by Cardinal Pinelli, and again by Fuga in the 18th century when some areas were re-laid. It is easy to tell which these are, as the year 1750 is included and also the quality is not so good as the original's. Also, the wide borders in white marble tiles around the Cosmatesque panels are 18th century. The work now includes a memorial slab for the cardinal, with his heraldry in polychrome inlay.