The works by El Greco and Francisco de Goya were discovered in the province of Alicante, Think Spain reported.
The paintings were reported missing in the late 1990s.
The Guardia Civil’s Historical Heritage squad uploaded photos of the missing paintings to an international database to alert police forces around the world of their disappearance.
Investigators received information about a possible sale of the two paintings, leading to a private address in the eastern city of Alicante.
“La Anunciacion” by El Greco and “La Aparicion de la Virgen del Pilar” by Goya were in several international exhibitions before being stolen.