The three-storey-high building was built around 1530-1535 on a rectangular plan. The ground floor and the undercroft have retained the original tripartite division, with the hallway providing the central axis. The connection of the northern and central bays on the first floor made it possible to set up the so-called 'grand hall': the palatium. Most probably due to a design change during the construction work, the level of the cellar floor was lowered which resulted in the exposing of the foundations made of white stone blocks in the cellars. The above ground sections of the walls and ceilings were made of brick. The hallway and the side bays of the ceilings received barrel vaulting. The side bays of the ground floor also had their ceilings, as did the hallway between them - this last a ceiling resting on beams as attested by the sockets for beams present in the coving of the current ceiling of the hallway. In the west, a small, centrally situated extension provided an antechamber to the main hallway, and perhaps also had a loggia connected to the grand hall of the first floor. The eastern front wall had four windows at the level of the ground floor and another four on the first; the northern wall had three, and the southern probably only two. Two cellar windows from that period at ground floor level have been preserved. They are both visible from the terrace and have stone frames and openings for a grating to be set in at an angle. This type of window can be found in the Renaissance architecture of Kanonicza Street in Kraków. The windows of the ground and first floors are set along an axis, which is a testimony to the modern character of the architectural solution applied. Six simple stone portals are preserved in what today is the cellar and which used to be the undercroft. Only one of these, positioned in the central bay whose threshold is set high above the level of the current cellar floor, has retained its original position. It leads to the Western extension, preserved only at cellar level. The remaining portals have been reset, possibly only lowered due to the transformation and lowering of the level of the cellar floor. A stone window jamb, exposed from under the render, has rich Renaissance profiling and sockets for the setting of a grate. This gives an idea of the decorative Renaissance framing of the windows on the ground and first floor levels of the residence.

A fundamental and certainly innovative element of Decius's 16-century design was the implementation of the full programme of a Renaissance villa and the application of pioneering architectonic solutions which provides proof of the Italian Renaissance contributing an era in Polish history.

In 1996, the Decius Villa was restored to its former splendour by an effort of the Municipality of Kraków. The Villa Decius Association, managing the villa and its park, continues with the humanist spirit of its patron and finds its objective in the development of a forum for the dialogue of cultures. In this way, it promotes pluralism and tolerance in public life, devoting special attention to the rights and cultures of national and ethnic minorities. To this end all the programmes of the Association are based on the idea of meetings between representatives of various fields of science and culture, nations, and areas of interest, as well as the idea of intellectual exchange and the pursuit of incentives to creative work.

The epitaph devoted to Anna Decjuszówna, the daughter of Iustus Ludovicius Decius, and to Andrzej Rottermund can be found in the Kraków Church of St Mary. It presents marble architectural decoration in the form of a cornice supported on pilasters terminating in Ionic capitals, with vegetal decoration. The line of the cornice is broken by a cartouche with the coat of arms of the Rottermunds (divided party per fess, with an anchor in the upper and carp in the lower field). The centrally situated figure presents a person praying before Christ crucified. It is one of the few material items related to the presence of Decius in Kraków.

Seweryn Boner, banker to King Sigismund the Old and a nephew of Jan Boner (one of the closest collaborators of Decius), was buried in the family chapel of St John the Baptist at Saint Mary's. The bronze tombstones of Seweryn (1538) and Zofia (after 1532) Boner, cast by the Hans Vischer workshop in Nuremberg, that are found in the chapel are believed to be among the best works of early Renaissance sculpture in Poland.