The 691 pieces were smuggled into Spain in 2003 by a man under investigation for suspected connections to Colombian drug cartels.
Police seized the 3,000-year-old busts, statues and stone jewellery in a raid as part of ‘Operation Florencia’ which looked into money-laundering by the drug gangs.
29 people were arrested, convicted, sent to prison and subsequently released after serving their sentences.
Throughout this time, the valuable haul was then stashed in Madrid's Museum of America while a complex legal battle was fought to determine its rightful owner.
A court finally decided on June 10th that the pieces should be handed over to Colombian authorities.
The collection is said to be of huge cultural and architectural value, according to local daily Madridiario.
The Colombian ambassador to Madrid, Fernando Carrillo Perez, said at a handing-over ceremony on Tuesday that the collection was the equivalent of “a museum coming to Colombia.”
Police General Director Ignacio Cosido said: “More than 95 per cent of the items are genuine.”
He added: “As well as their economic value, the pieces' greatest value comes from their roots, which is an expression of history itself, of culture and of every nation's soul.”
The rightful owners of 300 other seized pieces have not yet been identified.