Antimicrobial resistance is a well-recognized global issue. Fungal co-cultivation has emerged as a promising way for antimicrobial drug discovery. In the context of this thesis, a miniaturized cultivation strategy compatible with untargeted metabolomics was developed to study fungal co-cultures. In order to gain a comprehensive view of the induction phenomena that occur in microbial co-cultures also at the volatile level, the previous strategy was adapted to Solid Phase Microextraction (SPME) vials for Gas Chromatography Mass Spectrometry (GC-MS) analysis. The obtained results suggest that these strategies are applicable to microbial co-cultures for the study of non-volatile and volatile molecular inductions and identify potential antimicrobial compounds. Moreover, an MS-based dereplication strategy was applied to explore the metabolome of Epicoccum nigrum and revealed several putatively novel compounds. The developed metabolomic profiling strategies and targeted isolation procedures provide innovative tools for the identification and purification of induced bioactive fungal metabolites.