This paper explores the intersection of digital technologies, sustainable agriculture, and biodiversity conservation within the framework of the European Green Deal. The study investigates how intelligent agricultural practices—enabled by digital tools such as sensors, AI, and IoT—can enhance soil health and conserve agrobiodiversity. A systematic literature review was conducted to map out current research trajectories, identify the taxonomic focus areas in biodiversity monitoring, and assess the integration of digital tools. Results show a significant upward trend in publications linking digitalization and sustainability in agriculture. Findings highlight that pollinators and soil biota dominate monitoring focus, while technologies like remote sensing and AI show increasing adoption. The study concludes that intelligent agriculture offers a path toward ecological and economic resilience in rural landscapes, aligning with the EU’s green transition agenda.