Plants represent a rich source of structurally diverse secondary metabolites, which can be exploited in the development of new clinically important compounds. Indeed, due to their biodiversity, medicinal plants represent the largest library of compounds that has ever existed. To date less than 1% of this vast biodiversity has been exploited in drug discovery, due to several factors, including the lack of an appropriate multidisciplinary perspective. Here we review the successful application of computer-aided methods in screening a unique and high-diversity in house collection library composed of around 1000 individual natural products, isolated mainly from indigenous plants collected in biodiversity-rich countries, especially of the tropics and subtropics, and enlarged with their semi-synthetic and synthetic derivatives, as well as plant material extracts, up to around 2000 components. During the last ten years, the in house library has provided several lead compounds that have been developed, and in some cases patented, as anticancer and antimicrobial agents. The main classes of the library are described, including (but not limited to) alkaloids, terpenoids, Diels–Alder-type adducts, isoflavones, chalcones, and cannabinoids. The main focus is on the chemical characteristics and biological activity of these identified compounds, with particular attention being given to those currently under patent or in the preclinical phase. We also assess the use of computer-aided methods in screening this unique and diverse in house collection of natural products that, over the last ten years, has provided some lead compounds that have been developed, and in some cases patented, as anticancer and antimicrobial agents. Finally, this review highlights the potential use of plant food extracts as a source of nutraceuticals and functional foods. The multidisciplinary approach described herein may further motivate research groups involved in natural product chemistry to potentially benefit from a limitless source of novel bioactive compounds.