The 25-year-old, who spent last season on loan at the Butarque stadium, has signed a five-year contract.
Omeruo joined Chelsea from Standard Liege in 2012 but never made a competitive appearance for the Premier League club.
He had loan spells with ADO Den Haag, Middlesbrough, Kasimpasa and Alanyaspor before spending 2018-19 in LaLiga.
"We would like to thank Kenneth for his service and wish him all the best for the future," Chelsea said in a statement announcing the deal.
Omeruo, who will wear the number four shirt with Leganes, could make his debut in their opening LaLiga fixture of the season against Osasuna on Saturday.