The wide availability of geospatial data from different sources makes it necessary to create systems that are able to use and integrate the data to generate added value. We propose a system architecture following FAIR principles (Findable, Accessible, Interoperable, Reusable) and state-of-the-art methodologies for a server-side web-based application that performs virtual data integration over data sources that implement geospatial information standards. The architecture extends the mediator-wrapper design pattern with additional components that provide the system with additional flexibility and modularity, much needed for modern web applications. The architecture is composed of the mask, which acts as the interface of the system towards external users; a mediator that handles processing and data integration logic; a set of wrappers that communicate with the external data sources; persistent storage to provide flexible configuration and metadata capabilities to the system; and messaging queue for enabling asynchronous processing. At the same time, the architecture’s components are divided into four layers, each one with a specific role: presentation, configuration, processing, and communication.