During the Gunboat War of 1807 to 1814, fortifications were built in at Næbbet,[3] southeast of Skjoldnæs Fyr, but in Søby itself the port remained little more than a primitive pile bridge where the ferry to Als could dock.

The steamship connection to Faaborg started in 1903, the port was further deepened in 1924, and in 1933 a fully improved ferry berth was built.

Two years earlier, Arthur Christian Jørgensen had established a workshop specializing in the repair and improvement of small ship engines, developing into a full shipyard in 1950 with around 30 men employed to build fishing boats.

A big redevelopment involving some 290,000 m² of the port area is scheduled to start in 2022 for completion in the summer of 2024.

The Fynshav route is operated since 15 August 2019 by the world's biggest electrically powered ferry, the environmentally friendly E-ferry Ellen[8] which was itself built in the shipyard here by Søby Værft.