The construction of the manor house was started in 1797 under the guidance of the architect Johann Georg Adam Berlitz. He used the neo-classical design by the Italian architect Giacomo Quarenghi and added side avant-corps to the building. The construction work was completed in 1802. An English style landscape park and complex of subsidiary buildings were added to the ensemble.

After the fall of the Venetian Republic, St Mark’s Basilica became a cathedral, the Palazzo Patriarcale was built as the new headquarters of the Patriarchate of Venice (former headquarter was San Pietro di Castello). In 1837, architect Lorenzo Santi started to work on the building. The construction ended in 1850.

From 1894 to 1903, the building was the residence of Giuseppe Melchiorre Sarto (1835-1914), who later became Pope Pius X.

The design and initial building work on the Napoleonic Wing dates from the years when Venice was part of the Kingdom of Italy (1806-1814) of which Napoleon was sovereign and his stepson, Eugene de Beauharnais, was Viceroy. The site had previously been occupied by the San Geminiano Church  – an ancient foundation that had been rebuilt in the mid-16th century by Jacopo Sansovino – and ran between the Procuratie Vecchie and Nuove, the two long arcades of buildings which extend the length of St. Mark’s Square and had housed the offices and residences of some of the most important political authorities of the Venetian Republic.