Management of Natural History collections, particularly paleontological collections, is usually structured around specimens. However, it might not be feasible when the collections are incorporated from sources where the whole cycle of specimen collection is unknown, making it hard to determine what fossils belong to a single specimen and if these specimens belong to a single fossil-assemblage, taxon or individual. The Sociedade de História Natural from Torres Vedras (Portugal) manages such collections using a management strategy approach based on the spatial location from where the fossils were found. To achieve this, we have implemented a methodology for field collection and developed a spatial database in PostgreSQL/PostGIS to manage the entire stages of paleontological collections management. On top of the database, a second layer of web services, Web GIS (Geographical Information System) applications, and desktop GIS, all based on QGIS, are also under development to facilitate access to data stored in the database to internal and external researchers and partners, as well public institutions. This effort is made in close collaboration with in-house actors and stakeholders and has yielded promising results. The development of this system provides four advantages: (i) it played an essential role in supporting the transfer of the collection to new storage facilities; (ii) it provides overviews of the distribution of the characteristics of the collections; (iii) it enhances institutional partnerships by providing consistent and reliable data and(iv) it supports the establishment and development of research lines.