A hundred members of the campaign group scaled the facade of the 21-story El Algarrobico hotel on a secluded beach and painted it black leaving the words "illegal hotel" visible in white.
The hotel has remained empty since it was built in 2006 near the city of Almería and has become a symbol of the rampant urbanisation of Spain's Mediterranean coast.
Judicial authorities have ordered its demolition several times but it still stands, in the protected Cabo de Gata natural park, enraging environmentalists.
"El Algarrobico has brought shame on the Andalusian government for its slowness to act," said the director of Greenpeace Spain Mario Rodriguez in a statement on Monday.
The stunt, which started on Sunday and took 24 hours to complete, mobilised more Greenpeace activists than any other single action by the group in 30 years of campaigning in Spain, the statement said.