Cork oak (Quercus suber L.) forests are emblematic Mediterranean socio-ecological systems, supporting biodiversity conservation, rural economies, cork production and cultural heritage. Their long-term sustainability depends on the vitality of adult trees and, critically, on successful natural regeneration, which ensures stand renewal and the continued provision of cork as a high-value non-wood forest product. This study was conducted within the R&D&I framework of the Mobilising Agenda TransForm – Digital Transformation of the Forestry Sector towards a Resilient, Low-Carbon Economy, supported by the Portuguese Recovery and Resilience Plan and NextGenerationEU funds. As part of the collaborative project Resilient Forest Management, a network of permanent plots has been established across Portugal to monitor forest dynamics and environmental responses. Within this framework, research and pilot plots located in cork oak forests in northern Portugal were used to assess tree- and stand-level dynamics, with particular focus on early regeneration processes. The main objectives were to assess natural regeneration dynamics and compare two sampling designs commonly used in ecological and forestry monitoring: Line Transects and Radial Clusters. Over the two-year study period, both methods were applied to evaluate acorn density, seedling emergence and seedling mortality. The results confirmed the central role of acorn availability in regeneration success and revealed clear differences between sampling approaches and demonstrated that sampling design can strongly influence regeneration estimates. In particular, less spatially representative methods may underestimate early regeneration patterns. The findings indicate that the Radial Cluster design provides a more representative and efficient assessment of cork oak regeneration than traditional line transects. Its adoption within the TransForm permanent plot network can therefore improve the robustness of regeneration monitoring and support the early detection of changes in stand dynamics. The study also highlights the complex interaction between biological, environmental and management drivers, including acorn production, drought stress and stand structure, particularly stand density. Years with high acorn production and favourable canopy conditions supported initial seedling emergence, but summer drought emerged as the main bottleneck for regeneration success. High temperatures, irregular rainfall and prolonged dry periods may severely limit seedling survival, while local soil constraints, such as compaction and low fertility, can further reduce recruitment potential. Overall, these results reinforce the importance of systematic and consistent monitoring of natural regeneration as a priority for adaptive cork oak forest management. In a context of increasing climatic variability and management pressures, reliable natural regeneration data are essential for identifying early warning signs of ecosystem decline, guiding timely management responses, safeguarding cork production, promoting stand resilience and preserving the ecological, economic and cultural legacy of cork oak landscapes.