Human mesenchymal stem cells are considered the golden standard for clinical application in regenerative medicine for their multilineage differentiation potential, best candidates to treat diseases such as osteoarthritis and osteogenesis imperfecta. In the past few years several molecules have been described to induce the hMSCs differentiation into osteo cell progenitors, mainly discovered by screening of single metabolites bioactivity. However, hMSCs osteogenic differentiation potential is still poor, and the discovery of differentiation inducers with high efficiency is needed. Thanks to automated processes, High Throughput Screening (HTS) strategies shorten the metabolites bioactivity investigation timeline, allowing testing of many molecules simultaneously. In this work, reliable assays for natural products bioactivity investigation detection were developed using HTS methodologies and validated by testing 15 purified compounds derived by marine fungi and sponges. The HTS cytotoxicity investigation using HepG2 cells allowed to test in a single experiment, 15 metabolites in 4 concentrations ranging from 1 to 20µM. Low cytotoxicity was detected for metabolites concentrations from 1 to 10µM and so set as treatment concentrations to be tested in further assays. Anti-inflammatory bioactivity was tested on THP1 cells triggered by LPS. Five out of 15 metabolites showed to prevent the LPS induced THP1 inflammatory activation by lowering the TNF-α production. The metabolites pro-osteogenic potential was investigated using hMSCs: their differentiation was evaluated by calcium mineralization after 10 days differentiation. Pro-osteogenic molecules were not detected in this screening, but the method validation represents a powerful tool for future natural product and synthetic molecules libraries screenings.