In Piazza Eremitani stands the complex of the Civic Museums which groups the Archaeological Museum and the Museum of Medieval and Modern Art. The Museums are housed in the cloisters of the former convent of the Eremitani friars. The Scrovegni Chapel and Palazzo Zuckermann are part of the complex.

The building designed by Franco Albini, a well-known architect who won the Olivetti Prize for Architecture in 1957, stands next to the surviving section of the Roman amphitheater between the Scrovegni Chapel and the Eremitani church. The exhibition itinerary of the Archaeological Museum begins with pre-Roman finds from the necropolis of Padua, dating from the eighth to the third century BC. the beautiful bust of Silenus, the refined funerary stone of the young dancer Claudia Toreuma and the monumental funerary shrine of the Volumnii. Other rooms are reserved for Etruscan, Greek and Italiot materials. Two Egyptian rooms are dedicated to the pioneer of Egyptology from Padua, Giovan Battista Belzoni. The cloister instead houses the rich lapidary collection, consisting of columns, trabeations, capitals, friezes, architectural elements, mostly found in the area of the Euganean Hills and Padua. In 2008, the section dedicated to the Via Annia was opened, the great road built in Roman times to connect north-eastern Italy to the rest of the peninsula's road network.