Amazonian biodiversity is widely recognized as one of the richest and most diverse in the world. Covering approximately 40% of Brazilian territory, the Amazonian biome harbors a flora rich in natural resources that can be sustainably exploited to generate new products and innovative processes. Biological databases have been built to aid in a better understanding of these areas, as well as in identifying possible applications of their biological resources. However, the fragmentation and dispersion of data on species, biomolecules, and digital structures of the Amazonian flora across multiple repositories hinders bioprospecting processes, since researchers need to consult various databases to obtain information. Therefore, the objective of this article is to present Moléculas da Amazônia, a database developed to unify information on the species present in the Amazonian flora, as well as data on biomolecules that can be found in these species. For this, Web Scraping and ETL (Extract, Transform and Load) techniques were used to collect, integrate, and store data provided by GBIF, NuBBEDB, NCBI, and ChEMBL. The methodology resulted in the initial mapping of 118 species, 40 of which are endemic, and the cataloging of more than 500 molecules. With this, the "Molecules of the Amazon" project becomes a strategic tool to accelerate the discovery of new drugs and bioproducts. By organizing the chemical knowledge of the forest and its geographic distribution, the initiative supports the bioeconomy and sustainable development, connecting the natural wealth of the Amazon to technological innovation.