Brussels has announced the EU NAVFOR Operational Headquarters will be moved from its long-time base on Northwood in North London to the Spanish coastal town of Rota after March 29, 2019.
The Maritime Security Centre Horn of Africa will also be relocated to the French city of Brest.
EU leaders also agreed to extend the missions’ mandate until December 2020 as they prepare for Britain’s EU departure.
Operational Atlanta was launched by Brussels in December 2008 in order to protect ships belonging to the World Food Programme and African Union Mission in Somalia, which has been at war with jihadist terror group Al-Shabaab.
It’s mandate was widened to help tackle piracy and armed robbery off the coast of Somalia and monitor fishing activities in the region.
British Operational Commander, Major General Charlie Stickland, will also leave his role to be replaced by Vice Admiral Antonio Martorell Lacave from the Spanish navy after Brexit.
Major General Stickland said: “The transition is being planned with the utmost consideration to ensure it is smooth and seamless with continued cooperation and collaboration with all stakeholders throughout the region.”
Operation Atalanta will be “conducting business as usual with the force headquarters and ships remaining deployed and conducting deterrence of piracy and protection of WFP shipping,” he added.
Attacks off the coast of Somalia have dropped in numbers over recent years. They peaked at 176 in 2011 to only seven in 2017.
Only one attack in the region has been recorded, according to the International Maritime Bureau.
It was no surprise Spain and France will become the missions’ home after launching their joint campaign for Rota and Brest to take over in March 2019.
The decision results in another loss for the Italian government who put Rome forward as a potential venue for the Operation Atalanta headquarters after already losing out on the bloc’s medicines agency.
The move is just one of a number of EU agencies leaving Britain because Brussels law doesn’t allow the bloc’s agencies to be located in third countries.
Last year, the London-based European Banking Authority and European Medicines Agency were awarded to Paris and Amsterdam.
Rome threatened to launch legal action after the European Medicines Agency to the Netherlands when it was announced the body’s new premises would not be ready in time.