Objectives: the aim of this study is to explore the secondary metabolites produced by the endophytic fungus Chaetomium sp. isolated from Scencio stapeliiformis (E. Phillips) as well as investigate the anticancer and antimicrobial activity of crude extracts, fractions and pure compounds. Methods: An endophytic fungus (Chaetomium sp.) was isolated from the aerial part of S. stapeliiformis (from Giza, Egypt). DNA sequencing analysis, morphological and chemotaxonomy investigations were used for taxonomic identification. Metabolomics tools and dereplication studies were employed to choose the optimum growth medium and conditions that produce the most significant metabolites. The crude extract of the optimal fungal culture of Chaetomium sp. was then fractionated using flash chromatography and medium pressure liquid chromatography (MPLC). The structure of the isolated compounds was determined on the basis of 1D, 2D NMR and mass spectrometry (HR-ESIMS) analysis. Results: The bioassay-guided isolation afforded five pure compounds; p-hydroxybenzaldehyde (1), Uracil (2), 3-benzyl-6-isobutyl piperazine-2,5-dione (3), Cyclo (L-Alanin-L-leucin) (4) and Cyclo-(L-proline-L-leucine) (5). Multivariate data analysis highlighted the most significant metabolites contributed to the measured bioactivity. All fungal extracts were tested for the anticancer activity but only 30 days LC extract of Chaetomium was active. The pure compounds were tested for their anticancer and antimicrobial activities. Compounds 3 and 5 exhibited a significant anti-trypanosomal activity while compounds 1, 2 and 5 effectively inhibited the growth of E-coli and Staphylococcus aureus. Conclusion: A combination of metabolomic- and bioassay-guided protocol can efficiently predict the putative biologically active metabolites during the first stage of fractionation.