The urgent need to mitigate greenhouse gas (GHG) emissions in agriculture has prompted the development of certification systems aimed at promoting sustainable and low carbon practices. Although several low carbon certification systems for agricultural products exist in the European Union (EU), their adequacy for accurately measuring, evaluating, reporting, and verifying agricultural emissions and sequestration as well as associated carbon/GHG reduction credits at the farm level remains limited. This study presents a standardized approach to low carbon certification of agricultural production developed under the ClimaMED LIFE project, focusing on the integration of field-site GHG measurements (CO2, CH4, N2O emissions) into the certification framework. In this context, a six-stage low carbon certification system that incorporates a Tier 3 methodology encompassing several innovative on-site data collection and analysis technologies such as Light Detection and Ranging (LiDAR) and Internet of Things (IoT) telemetry is proposed. This integrated approach has been developed for five agricultural products, i.e. olive trees, grapes, cereals, pistachios and vegetables cultivated in the Mediterranean region based on several low-carbon practices implemented and monitored at farm level (15 pilot fields in total). This study also explores the challenges and opportunities associated with implementing such an integrated framework, considering technological, economic, and policy dimensions. The proposed framework shows significant potential as a valuable tool that can be easily adapted to several agricultural products to assist public authorities, policymakers, certification bodies, and agricultural stakeholders seeking to establish a robust and transparent certification system for evaluating and endorsing low carbon practices. This framework is expected to drive the broader incorporation of innovative technologies to accurately measure, monitor and report carbon/GHG reduction credits and promote the establishment of similar certification systems in various other sectors.