Natural products (NPs) have traditionally played an important role in drug discovery, contributing to major medical breakthroughs such as penicillin. However, despite progress, diseases with poor prognoses persist and emerging health threats, such as antibiotic-resistant infections, highlight the continued need for new molecules in drug discovery pipelines. While synthetic compound libraries dominate high-throughput screening, natural product (NP) research remains active. Biotransformation, the use of living organisms or enzymes to chemically transform compounds, offers a promising alternative to the classical NP isolation approach. This thesis explores a new strategy using fungal secreted enzymes (secretome), specifically from Botrytis cinerea, to generate diverse NP derivatives. State-of-the-art techniques allowed the isolation and characterization of 107 compounds, 69 of which were described for the first time. Screening against several biological targets revealed a range of activities, including promising antibacterial activity. This thesis also explored whole-cell biotransformation using living fungi, demonstrating adaptability to a miniaturized 96-well plate format for increased throughput. The strategies developed, although mainly focused on a single fungal species, have the potential to build libraries of NP-like compounds for screening, potentially allowing the discovery of promising biological activities.