The aim of this study was the investigation of the metabolic profile of the biologically active endophytic strains of the Egyptian medicinal plant Bidens pilosa and the isolation and structure elucidation of their bioactive constituents. Eleven different fungal strains were isolated from the different plant parts. Bioactive strains were chosen for chemical investigations. Activity-guided fractionation resulted in the isolation and structure elucidation of 25 compounds. The extract of a Botryosphaeria rhodina strain yielded four new depsidones, botryorhodines A–D and a new diphenyl ether (botryorhodine E). An Aspergillus neoniger strain extract yielded four known naphthopyrones: aurasperone A, asperpyrone D, dianhydroaurasperone C, and aurasperone D, as well as two diketopiperazine dimers, asperazine and a new asperazine analogue (asperazine A). From the extract of a Khuskia oryzae strain two oxylipins were identified, one of them was found to be new. A plant immune assay was carried out on all endophytic fungal extracts to test for the presence of elicitors of immune response of the model plant Arabidopsis thaliana. To examine the interaction between the endophytes, the strain extracts exerting antifungal activity were tested for their effects on the growth of the other endophytic strains in agar diffusion assays. Results of this study suggest that the endophytes of B. pilosa contribute to the known dominance of this plant through their bioactive metabolites. The one meter height observed for the plant is most probably stimulated by the production of the auxin indole carboxylic acid by all its endophytic strains. The antifungal activity of some secondary metabolites against phytopathogens suggests a plant protective effect exerted by the endophytes.