The lab, found in the rural area of Soacha, is the closest of its kind ever to have been discovered so close to the capital.
Two suspects were captured at the scene and charged with the illegal trafficking of substances used in cocaine production.
The anti-narcotics unit will now try to establish which criminal group is responsible.
Potassium permanganate, one of the substances found at the scene, is an oxidising agent necessary to create cocaine hydrochloride, the powder form of the drug in its purest form before it is adulterated by cutting agents at street level.
Colombia remains the largest producer of cocaine in the world, with 90% of the drug seized in the U.S. originating from the country, according to the U.S. State department.