Methods for estimating carbon storage in agricultural and forest soils. State of the art and experts opinions

Synthesis

Disclaimer: The content of this publication is based on the state of knowledge and the regulatory framework in force at the time of publication of the documents.

Context of the Study

This study stands at the intersection of scientific advances in the understanding of soil carbon in agricultural and forest ecosystems, the evolution of public policies and legislative frameworks, and emerging economic strategies that increasingly incorporate the role of soils in climate change mitigation. The measurement and certification of soil organic carbon contents and stocks (SOC and SOCS) are used primarily as tools to monitor and assess land management strategies implemented at local scales or public policies at various levels. They are also becoming levers for financing the transition through carbon markets and payments for environmental services. These mechanisms require rigorous scientific approaches based on in situ measurement and laboratory analyses, often combined with empirical or mechanistic modelling of SOC and SOCS dynamics. Within this triangle of science, public policies, and economic strategies, the core challenge remains to ensure the credibility, transparency, and traceability of soil carbon stock or avoidance emissions estimates.

Objective and Study Plan

The main objective of this study is to provide an informed assessment of existing methodologies for quantifying soil organic carbon, identifying the main sources of uncertainties that limit their use in carbon certification and remuneration schemes or their operational translation into public policies and regulatory texts. The study also aims to propose methodological recommendations that ensure scientific robustness and fairness in any associated remuneration. It is structured around four axes : (1) a (non-exhaustive) overview of international, European, and French national initiatives related to soil carbon measurement and certification, (2) a critical analysis of quantification approaches, including direct measurement, modelling, and emerging complementary methods, (3) case studies illustrating challenges and potential leverage points, and (4) a synthesis of results leading to operational recommendations for project developers or public and private decision-makers.

Presentation of Main Results

This synthesis, based on a non-exhaustive analysis of about sixty documents, aimed to identify the role of soil organic carbon in public policies, incentive schemes, and economic strategies, whether or not they already stem from regulatory texts (Axis 1).

The analysis highlights a clear evolution in the perception of carbon, initially focused on carbon dioxide (CO₂) as an indicator of greenhouse gas (GHG) emissions and mitigation efforts. Since the 1992 Rio Earth Summit, where the three major environmental conventions (UNFCCC, UNCCD, CBD) were adopted, soils have been recognized for their ecological importance, but their climate role (as carbon sinks or sources) remained neither quantified nor integrated into monitoring mechanisms. The 1997 Kyoto Protocol was the first milestone in which soil carbon storage became part of climate policy, notably through Articles 3.3 and 3.4, recognizing activities related to Land Use, Land-Use Change and Forestry (LULUCF). These articles frame GHG emissions and removals from afforestation, reforestation, deforestation, and forest, cropland, and grassland management. Agricultural and forest soils were thus formally incorporated into national carbon accounting. Methodological consolidation came with the IPCC Guidelines (2006) and the recognition of the AFOLU sector (Agriculture, Forestry and Other Land Use), which combined LULUCF and Agriculture, reflecting carbon fluxes between soil, biomass, and the atmosphere. After 2015, declared as the «International Year of Soils», soils gradually gained recognition in public policies: soil organic carbon is now acknowledged as an indicator of soil health and ecosystem resilience and is central to sustainable management and restoration policies. More recent developments also emphasize soil-related climate adaptation. Several European and national regulations describing quantification methodologies at specific scales or sectors are analyzed in this study: Regulation (EU) 2018/841 (LULUCF), Regulation (EU) 2018/1999 (Governance), Directive (EU) 2018/2001 (RED II), Implementing Regulation (EU) 2022/996, Regulation (EU) 2023/839 and French Decree n°2018-1043. They address in situ measurement, laboratory analyses, and modelling following IPCC Tier 1 to Tier 3 approaches (2006, 2019).

For the contracting authorities of this study, the aim is to use these quantification methods with varying levels of detail while integrating risk and uncertainty management and anticipating emerging regulations. Soil carbon storage has now been integrated into corporate social responsibility (CSR) and ESG reporting, in line with the CSRD directive. Quantification aspects are essential to meet the expectations of investors, consumers, and society at large. Proactive ESG management enhances reputation, sustainable performance, and transparency in relation to soil organic carbon. In a context where carbon reductions, avoidance, or storage gain monetary value on regulatory or voluntary markets, the key challenge is credibility and comparability of carbon estimates.

The study highlights the complexity of the institutional framework (national and European), marked by the coexistence of sectoral public policies, funding schemes, and voluntary initiatives. Carbon quantification now extends across entire value chains, including agricultural, forestry, and energy sectors. To help project developers navigate this complexity, the study proposes a structuring diagram and a project-guidance table that identify key steps and guiding questions. The aim is not to provide a single method, but a framework that enables the selection of the most relevant approaches. Missing answers to certain questions should drive actors toward appropriate contacts or support mechanisms.

In doing so, the synthesis highlights a converging movement between science, regulation, and economic strategies, where soil organic carbon valuation becomes both an environmental and a financial strategic lever, creating the concept of «carbon farming». Recognizing the multifunctionality of soils and increasing requirements for traceability call for integrated carbon governance founded on scientific reliability, data transparency, and coherence between policy and economic instruments (e.g. Common Agricultural Policy, Renewable Energy Directive, Soil Monitoring and Resilience Directive, Carbon Removal Certification Framework, and labelling or certification tools).

Drawing on key scientific publications (e.g. Pellerin et al. 2021, Don et al. 2024), existing standards and guidelines (IPCC 2019, FAO GSOC MRV Protocol 2020, NF X 31-100 2020, ISO 23400 2021, etc.), ongoing research, and external expert advice, the study first redefines soil carbon terminology: content, stock, storage, sequestration, stabilization, permanence, flux, emissions, reductions, etc. This component also presents the analyzed methodologies through four sets of summary sheets:

• soil sampling and field collection related to existing standards and guidelines and to the recommendations identified in Axis 1;
• laboratory analyses for SOC measurement, covering routine methods (dry combustion, Walkley-Black oxidation) and emerging techniques (e.g. RockEval®);
• uncertainties and their propagation, with emphasis on detectability of changes in SOC stocks;
• modelling of carbon stock dynamics, presenting a range of mechanistic models and associated uncertainty analyses.

Although seemingly simple, estimating soil organic carbon stocks (SOCS) relies on an equation involving several parameters: SOC content, bulk density, sampling depth, and coarse fragments content, each carrying uncertainties that propagate into the final calculation. Spatial variability, often high even within a single field and especially in forest environments, reinforces the need for intensive sampling, sometimes requiring dozens to hundreds of samples. Even when using composite samples, accuracy strongly depends on the number and distribution of sampling points.

Regarding dynamics, correctly interpreting stock changes requires that compared plots share equivalent initial conditions, in line with IPCC guidelines and regulatory frameworks, which mandate the use of baseline values. Databases such as RMQS or LUCAS Soil can provide such baselines, but the most reliable approach remains direct measurement of a shared initial state, accompanied by detailed pedological characterization (profile description, texture, oxides, chemical analyses) and carbon assessments on clearly defined horizons. This requirement applies equally to monitoring a single plot over time, where the baseline should be measured on-site rather than derived from generic values. Moreover, because SOC changes are slow and modest, statistically detecting significant differences over less than a decade remains challenging and requires an initial or baseline field diagnosis that may be costly but necessary.

Harmonized sampling and analytical protocols, consistently applied over time, are therefore essential for temporal comparability. Rigorous implementation, combined with quality control in the field and laboratory, ensures scientific validity. Operator expertise, the use of certified reference materials, and metrological verification of equipment contribute to reliable results. Laboratories play a central role by ensuring traceability, repeatability, and comparability of analyses, and by participating in inter-laboratory programs that improve accuracy and reduce uncertainties.

Several emerging quantification methods are presented (VNIRS, RockEval®, remote sensing), but they are currently used mainly in research. Remote sensing and artificial intelligence, in particular, open promising perspectives for soil carbon quantification. Although not yet operational, they show strong potential. Work by CESBIO, especially via the Agri-Carbon-EO methodology, demonstrates that satellite-based analysis of vegetation cover growth can effectively complement SOC dynamics models, improving precision and spatial resolution of SOCS monitoring.

Analysis and Commentary on Results

The analysis and discussion build on two case studies:

• Case 1: Directive RED II (EU) 2018/2001 and its 2023 update, together with Implementing Regulation (EU) 2022/996, define bioenergy sustainability criteria including impacts on soil carbon stocks: application to the biomethane sector.
• Case 2: The French «Label bas-carbone» (Decree n°2018-1043), based on standardized and verifiable calculation methods: application to a low-carbon agriculture project (Arable crop systems methodology: LBC-GC).

The case studies illustrate the inherent difficulty of measuring carbon stocks and the strong influence of initial conditions (soil type, climate, «carbon-sequestering» practices, measurement precision, etc.) on measured values and expected variability. They also clarify the role of mechanistic modelling (TIER 3) while accounting for model uncertainties.

Case 1. Methanization and the eSCA calculation

The study highlights the sensitivity of the eSCA calculation (emissions reductions due to carbon accumulation in soils) to uncertainties linked to field measurements of SOC stocks (CSR and CSA). Real effects of carbon-sequestering practices, such as reduced tillage, occur slowly and often within shallow horizons (0-10 cm). The 0-30 cm depth used in protocols remains relevant for medium- and long-term monitoring.

Comparison of the studied situations shows that soil type influences eSCA values as much as, or more than, crop management practices themselves. In practice, biomass supply considerations for biomethane production cannot rely solely on this criterion.

Moreover, eSCA calculation reflects carbon dynamics of an entire cropping system, including both energy and food crops. Attributing the entire system-wide carbon storage to the unit of energy produced results in crediting energy crops with storage generated partly by other crops in the rotation, creating an allocation bias. The study therefore recommends revising the eSCA equation to better distribute each crop’s contribution.

The calculation also assumes that the reference stock (CSR) corresponds to an equilibrium state. When this is not the case, it becomes difficult to attribute all observed storage to the innovative scenario alone.

To overcome these limitations, the study proposes aligning the method with the «Label bas-carbone» for the Arable crop Systems approach (LBC-GC), based on differential modelling of carbon storage (project vs. reference scenario) over 5-10 years. This would enable fairer crop allocation and stronger consistency with MRV requirements.

Implementation would rely on:

• robust simulation models validated with long-term datasets,
• improved SOC stock measurement systems (CSR and CSA),
• satellite technologies to verify crops and biomass,
• continuous eSCA monitoring on experimental sites,
• technical and human support for farmers, backed by supply chains,
• and attention to the redistribution of benefits among energy-sector stakeholders.

Case 2. Label bas-carbone: Arable Crops

The LBC-GC (v1) project illustrates the role of agronomic levers in reducing GHG emissions at the cropping-system scale. Reductions are modest but significant, strongly depending on practices affecting soil carbon inputs. Both the reference and alternative systems (including a cover crop in the project scenario) show a tendency to accumulate SOC, though more strongly in the project system (+6.5 tSOC/ha after 20 years). Dynamics may vary depending on pedological characteristics (calcareous soils, initial SOC levels). The LBC-GC methodology is less sensitive to soil measurement uncertainties because it relies on scenario comparison rather than absolute field measurements, an important advantage over eSCA, in its actual calculation form.

This approach encourages farmers to adopt improved practices even when immediate net storage is limited, by rewarding relative progress. Strengthening incentives to maintain long-term SOC enhancing practices would be beneficial, given their agronomic and ecological advantages.

Finally, the robustness of the LBC-GC system depends heavily on the quality of soil organic carbon balance models (e.g. AMG). These models must continue to be refined through research and R&D to increase accuracy and applicability. Even though modelling reduces uncertainty relative to direct measurement, uncertainties remain tied to input data quality (yields, cover-crop biomass, organic amendments, etc.).

Conclusions

The study underscores the need for an integrated approach combining scientific rigor, operational pragmatism, and recognition of environmental co-benefits. While direct SOC measurement remains essential, it must be accompanied by harmonized protocols, robust modelling tools, and transparent governance of results and uncertainties. The study, like ongoing research, highlights the substantial uncertainties and difficulty of detecting significant SOC changes. Scientific robustness in carbon-stock change calculations therefore requires long timeframes, extensive sampling, strict protocols, and validated models across varied pedoclimatic contexts. Without these conditions and consistent protocols between baseline and follow-up states (+5, +10, +15 years), using such estimates as the basis for remuneration mechanisms becomes questionable.

A comprehensive approach must also recognize the agro-ecological co-benefits of increased SOC: biodiversity, water retention, regulation of the water cycle, erosion control, and climate resilience. Farmers and land managers adopt system changes for multiple benefits, not solely to store carbon. Their decisions incorporate improvements to their farm-level carbon footprint and to the carbon performance of products sold to industry or markets, alongside wider socioeconomic and environmental goals. It is in this broader context that the transition toward low-carbon agriculture will find realistic and lasting pathways. Carbon is a useful but insufficient indicator: overly focusing on it risks overshadowing other benefits and introducing biases. For credible, fair, and effective systems, integrating these co-benefits into broader agro-ecological remuneration schemes is advisable, reducing reliance on complex measurements and supporting a systemic and holistic approach aligned with societal and climate objectives.