The Chromolaena genus is composed by about 170 plant species widely distributed in tropical areas. Several kinds of secondary metabolites and different biological activities have been described for species belonging to Chromolaena. This work described, for the first time, the phytochemical analysis of different polarity leaf and flower extracts of the Colombian species Chromolaena scabra (LF) R. King & H. Rob. Conducted assays resulted in the purification and identification of fatty acids derivatives, steroids, a diterpene, and flavonoid metabolites. The preliminary phytochemical analysis revealed the presence of the main groups of secondary metabolites: steroids, triterpenes, carotenoids, alkaloids, tannins, and flavonoids. In parallel, the antifungal activity of these C. scabra leaf and flower extracts against the fungus Fusarium oxysporum f. sp. lycopersici, was determined.