The building, built around 1786, is one of the best examples of Maltese architecture as it belongs to the transitional phase from the Baroque to Neo-classical. It was commissioned by the Noble Gio Francesco Bonnici, Baron of Qlejjgħa as a summer residence.

Originally known as Villino Agata, it has an uncommon layout since the main façade of the property is considerably set-back to accommodate the gardens, while the back façade abutts onto Argotti Street. Today, the front part of the garden is built and Villino Agata is not visible from Vincenzo Bugeja Street (formerly San Calcedonius Street).

The architect was the Italian Stefano Ittar, also commissioned to build the Bibliotheca in Valletta. In fact there are some similarities between the façades of the Bibliotheca and Villino Agata.

Villino Agata has the same divisions on the façade as that of the Bibliotheca. It has five vertical bays separated by pilasters and with recessed panels for the windows. The window and doorway openings at first floor level have triangular pediments as those of the Bibliotheca. The ground floor doors have a moulded arched pediment above heavily decorative floral motifs around a number of faces and a ram’s head. The centrally imposing pediment at roof level forms part of the moulded cornice that crowns the building.

The balustraded parapet wall is centrally punctured to accommodate the escutcheon having an elaborate coat-of-arms and a crown. According to Hughes et al. (2003), this façade is more Baroque in nature than Neo-classical unlike the back façade of Villino Agata.

The rear façade in Triq Argotti is rather Neo-classical having heavily projecting mouldings around the main entrance that support heavily decorated corbels. These corbels support a closed masonry balcony. Unfortunately, the original balcony has been replaced with a closed masonry balcony of poor design.

Villa D’Agata was included in the Antiquities Protection List of 1932 and scheduled by Mepa as a Grade 1 national monument as per Government Notice number 1082/09 in the Government Gazette dated December 22, 2009.