The EU-funded DIONE project (grant agreement No. 870378) offers an innovative close-to-market (TRL7) solution seeking to improve the traditional methods of agricultural monitoring. The project introduces a cloud-based Software as a Service (SaaS) system architecture, building on a fusion of novel technologies that will support the forthcoming needs of the modernized Common Agriculture Policy (CAP) and the "Greening" perspectives, with an automated area-based monitoring system. In particular, an interoperable and harmonized system is designed, connecting large volumes of Earth Observation data (Satellite, UAV, and in-situ) and user-generated highly precise geolocated data (geo-tagged photos, soil measurements, etc.). DIONE's system architecture encompasses customized and third-party frameworks, where heterogeneous and multi-source data are stored, processed and managed using Artificial Intelligence (AI) algorithms. These harmonized, curated and open accessed data are then provided as Open Geospatial Consortium (OGC)-compliant, web-service layers (WMS, WFS, and WCS). Furthermore, the proposed solution formulates a scalable, flexible, interoperable, and semantically enriched environment, taking advantage of a Spatial Data Infrastructure (SDI) framework capabilities, whilst allowing an interactive connection among different tools and components through RESTful APIs. Our approach establishes a novel, cloud-based, accurate and inexpensive agriculture monitoring solution, enabling the real-time provision of multi-source data to relevant stakeholders such as Paying Agencies, Policy Officers and Control & Certification Bodies, and other domain experts. The system architecture was formulated exploiting a codesign methodology, aiming to ensure a long-term and sustainable solution. Two large scale demonstration will take place in Lithuania and Cyprus, evaluating the system capabilities in real-life and operational conditions.