The drugs squad seized Cipriam Manuel Palencia Gonzalez, 34 — alias "Visaje" — under an international arrest warrant for homicide, a police statement said.
"Palencia Gonzalez is considered the main leader of Los Urabenos, a Colombian paramilitary organisation, and responsible for ordering a plan to murder officers of the Colombian national police," it said.
He is accused of drug-smuggling, extorsion and several killings, including ordering attacks that left one Colombia police officer dead and another seriously wounded.
Los Urabenos is considered by Colombian authorities to be one of the most dangerous gangs in the country.
It is partly manned by former members of paramilitary groups that were formed in the 1980s to fight against leftist guerillas in the country's long civil conflict and were disbanded between 2003 and 2006.
Spanish officers arrested Palencia Gonzalez in Madrid, where he was suspected to be organising new drug-trafficking operations.
He had escaped from jail in Colombia in 2009 and in September this year fled wounded from a police raid in which a policeman was killed and six members of the gang were arrested.
Spain is one of the principal entry points for illegal narcotics into Europe. Colombia is one of the world's biggest sources of cocaine: it produced 309 tonnes of the drug in 2012, according to the United Nations Office on Drugs and Crime.