The building has characteristics typically attributable to the construction modules of the second Renaissance and has a typically Emilian architecture.
Palazzo Pepoli was not born in the form and distributional and structural organization in which it presents itself to our eyes today, but it is a harmonious architectural project resulting from profound transformations and expansions. Its final structural determination is in fact the result of a series of important transformation works carried out over the course of over a century, between the end of the 1500s and the end of the 1600s.

Furthermore, the cellars of the Palace have highlighted complex underground brick structures, pre-existing the construction of the building and attributable to interventions carried out in different periods.

The sculptural decorations that adorn it are hypothesized to have been created by the sculptor and plasterer Giovan Francesco Bezzi, who had already collaborated with the architect Torri on some buildings in Bologna.

One of the most important architectural elements of the entire building is represented by the helical staircase, the most successful example of this typology due to its dynamic sense and proportions. It presents a body of high architectural plasticity and structural lightness, yet with a high functional performance such as to guarantee the connection between the different floors. Its starting point is the basement of the building, and then extends with its helical and almost hypnotic effect, up to the attic rooms for a height of approximately 17 meters and 107 steps in pink Verona marble. All completed by a light and stylistically harmonious wrought iron railing.

The hall of honor characterized by a majestic vaulted ceiling, decorated with swans (emblem of the Pepoli family), angels with trumpets, cherubs and masks, stylistically contrasts with the atmosphere of the basement of the Palace, to flow into the majesty of the Baroque with the its architectural games, the plasticity of the suspended decorations, the soft colours.

Located on the mezzanine floor and placed in an asymmetrical position with respect to the entire structure, it was certainly the fulcrum of the cultural life of the Palace.

The main hall is also characterized by a wooden balustrade also of Baroque appeal and from a functional point of view it has the purpose of creating a connection between the eight rooms on the first floor of the building.

The first floor has three rooms in the west wing and five in the east wing, different in style and architecture, almost as if to signify a different use. The rooms to the west are characterized by simpler and more sober lines which contrast with the decorations, bas-reliefs, vestments and stuccos of the rooms to the east. The different function is also demonstrated by the floors: as regards the main hall, Venetian style flooring was created, while for the other rooms, terracotta floors with square tiles.