After the end of the Este era, the Palazzo dei Musei was considered the ideal place for all the various records of Modena's history. The city Archive, previously housed in the Palazzo Comunale, and before that in a room in the Ghirlandina tower, was moved there in the late XIX Century. The Archive contains the documents recording political and administrative events in Modena as a city state, as the capital of the Este state and as an Italian municipality, covering a period of time which ranges from the XII to the XX Century (although the oldest item dates from as far back as 969). It is also the repository for the records of defunct charitable foundations and private archives, as well as manuscript Chronicles of the city, rare manuscripts and letters by famous people. It includes a library with incunabula, XV Century editions and rare books from the XVII and XVIII Centuries amongst its oldest texts, and a collection of local periodicals and daily papers begun in the XVIII Century. A reading room is open daily for researchers. In addition, in 1886 the City Council decided to use the third floor of the building to house objects and historic finds formerly kept at a variety of locations around the city. In 1962, this material was divided to provide the core of today's Museo Archeologico Etnologico and Museo di Arte Medievale e Moderna. Renovation work in the early '90s transformed the premises, the cupboards and display cases, and the layout of the materials, creating a permanent exhibition which is attractive in itself, regardless of the value of the pieces on show. The room of the archaeological sector, divided into three sections by two lines of pillars, with a cross-vaulted ceiling and housing large glass-fronted cabinets, is particularly striking. The exhibits in the Medieval and Modern Art sector are especially interesting because most of them are of local origin and give a more concrete sense of the city's history. The 1st room, containing paintings and prints of the Modena of bygone days, offers fascinating insight into the city's development. The 2nd room is dominated by the work of Begarelli, with his Madonna di Piazza and a small Head of an Angel. The Madonna, Begarelli's first documented work produced when he was twenty years old, already shows the influence of Raphael's classicism. For almost three centuries it occupied a niche in the Palazzo Comunale, but it was removed in 1798 in obedience to a decree which banned the presence of religious images in public buildings. Alongside, two scagliola altar-frontals and two sculpted holy water stoups reflect the Carpi tradition of "mischia" work and the Medieval religious spirit.

These exhibits are followed in the 3rd room by brasses, in the 4th by architectural brickwork and woodcut maps, in the 5th by scientific instruments, in the 6th by the pottery and majolicas of the Ferrari-Moreni factory at Sassuolo, and in the 7th by weaponry, bits for horses and a single-seater carriage . The last room contains the Gandini Collection, unique of its kind in Italy, of over 2000 fragments of fabrics produced between the XI and the XIX Centuries. The Museum of Archaeology and Ethnology opens with a room dedicated to Archaeology, with exhibits found locally dating from the Old Stone Age and above all the New Stone and Iron Ages. The most famous item is the Venere di Savignano, of such value that the object on display is only a copy. The section dedicated to the Roman Era contains the Bassorilievo dei Niobidi (II Century A.D.) and the Domus bronze furnishings found in via Università. The Etruscan exhibits include votive bronzes, funerary urns and a large bronze situla. The three rooms of the Ethnography sector house materials from New Guinea, from pre-Colombian Peru, from South America, from Africa and from Asia. The first room is especially interesting, since the stone axe-heads with wooden handles provide a useful comparison with the exhibits in the archaeological sector.