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Biodiversity crisis calls for better knowledge of the status of biodiversity, but also drivers and pressures behind the ecosystem change and the vulnerability of habitats. There is growing demand for the biodiversity data for decision-making on national, regional and global scales. However, the operationalized biodiversity and ecosystem monitoring systems which can integrate remote sensing, in situ and modelling data are still rare despite of that there are good co-operation initiatives such as Australian TERN and US NEON in place. In Finland, we have launched the Finnish Ecosystem Observatory (FEO) as a reaction to such a need to upgrade and modernize biodiversity and ecosystem monitoring schemes. We have started a development of national research and monitoring infrastructure/platform which can integrate different data types and provide timely data and knowledge for various decision-making purposes. In this short paper, we describe three case studies as examples of different data types and different monitoring needs: i) habitat mapping for large area, ii) hydrological condition of aapa mires, and iii) automated Aspen mapping for boreal forests. We will evaluate the possibilities to operationalize the production of such data sets in a long-term as well as the challenges and bottlenecks related either to data, processing or applicability. Finally, we will also discuss how FEO and similar kind of biodiversity monitoring platforms could be further developed, and how the network of such observatories could co-operate in the future.