Pylos has been inhabited since Neolithic times. It was a significant kingdom in Mycenaean Greece, with the remains of the so-called "Palace of Nestor" excavated nearby, named after Nestor, the king of Pylos in Homer's Iliad. During the Peloponnesian War, the Bay of Pylos was the site of the Battle of Sphacteria in 425 BC.

In the Middle Ages, during the time of the Crusades, Pylos fell to the Principality of Achaia, founded in 1205. In the 1280s the Franks built the Old Navarino castle. Pylos came under the control of the Republic of Venice from 1417 until 1500, when it was conquered by the Ottoman Empire.

The Ottomans used Pylos and its bay as a naval base, and built the New Navarino / Niokastro fortress there. The area remained under Ottoman control, with the exception of a brief period of renewed Venetian rule from 1685–1715 and a Russian occupation from 1770–71, until the outbreak of the Greek War of Independence in 1821.

The church of the Transfiguration of Christ occupies a central place inside the Niokastro in Pylos. It was originally built as a mosque during the reign of sultan Murad III (1573-1595). During renewed Venetian rule it was turned into a catholic church. After the re-conquest of the castle by the Ottomans it is likely that the building was again used as a mosque. In 1770, during the Orlov revolt, it was turned into a christian orthodox church. The church was used as an ammunition depot by the French troops at Niokastro (1828-1830) and after that, until 1842.