Admiral Andrea Doria provided his villa with splendid gardens, suitable for the importance of his residence, overlooking the sea to the south, and laid out in a series of terraces climbing the steep hill of Granarolo to the north. Perin del Vaga was in charge of the initial layout of the spaces in the garden: from that first project still remains today the Dolphin Fountain, made by Silvio Corsini to a design by the Florentine artist. Andrea later turned to Giovanni Angelo Montorsoli, who oversaw the arrangement of the northern garden, now completely lost, and created the Satyr Riding a Dolphin sculpted group, still visible in the south garden.

Andrea's heir, Giovanni Andrea I, was responsible for the final arrangement of the historical site. The most spectacular work commissioned by Doria was a magnificent aviary in which peacocks, pheasants and rare birds nested. At the end of the 16th century, Taddeo Carlone created the Fountain of Neptune, which is still today the centrepiece of the Italian garden.

Over the following centuries, the garden’s appearance was altered by the various interventions and modifications it underwent. In the 1630s, the construction of sea walls by the Republic blocked its direct view over the sea. The 1760s, coinciding with the transfer of the Doria Pamphilj family's main residence to Rome, marked the beginning of a period of steady decline.

During the 19th century Prince Filippo Andrea V and his wife Mary Talbot initiated a renovation of the garden, following the forms of the romantic English style, which required the removal of the symmetrical layout typical of the Italian garden. The north garden was compromised mid-century by the construction of the Genoa-Turin railway line.

The 20th century saw an extensive series of works which significantly altered the area surrounding the Villa del Principe, beginning with the building of the new Stazione Marittima (Ship Terminal), of Via Adua (in the Thirties) and of the elevated highway (1962-65). In 1944, the bombings of the Second World War caused major damage to both the Palazzo and the garden.

The garden in its current form is the result of a restoration project which brought back the layout of the 16th-century garden, the time when the Villa and the family were at the height of their fame.