Here we describe an innovative platform which combines the use of the nematode Caenorhabditis elegans, as validated in vivo model for compound screening, with the first laboratory device for its fully automated in vitro culture, treatment and multi-parametric analysis. Our microfluidic device allows automated high-content phenotyping of C. elegans, via accurate control of worm culture conditions and real-time automated monitoring of multiple physiological parameters. This screening format could be readily used to identify toxicity effects of substances, associated to specific phenotypic responses in the worms, within only 4 days. We employed our platform for screening organo-metallic photovoltaic perovskites, which are making a breakthrough in light-to-electricity conversion efficiency. Our results show that two of the most studied photovoltaic perovskites, CN3NH3PbI3 and CN3NH3SnI3, may significantly impact development, fertility and survival of C. elegans, even at relatively low concentrations. Given the exponentially growing rate at which application-oriented novel compounds emerge every year, our technology is expected to become a new important tool for the rapid in vivo assessment of potential health hazards of new compounds before any large-scale production. In conclusion, we propose an innovative solution for rapid identification of toxic compounds, using a biological model that perfectly bridges the gap between in vitro and in vivo assays.