Soil carbon storage is a well identified climate change mitigation solution. The extensive in-situ monitoring of the soil carbon storage in cropland for agricultural policy and offset carbon markets is prohibitive, especially at intra-field scale. For this reason, comprehensive Monitoring, Reporting and Verification (MRV) of soil carbon and its explanatory variables at large scale needs to rely on remote sensing and modelling tools that provide the spatio-temporal dynamics of the carbon budget and it’s components at high resolution with associated uncertainties. In this paper, we present AgriCarbon-EO v1.0: an end-to-end processing chain that enables the estimation of carbon budget components of major crops and cover crops at intra-field resolution (10 m) and large scale (over 110×110 km) by assimilating remote sensing data in physically-based radiative transfert and agronomic models. The data assimilation in AgriCarbon-EO is based on a novel Bayesian approach that combines Normalised Importance Sampling (NIS) and Look-Up Table (LUT) generation. This approach propagates the 10 m uncertainties across the processing chain from the reflectances to the output variables. The chain considers as input a land cover map, multi-spectral reflectance maps from the Sentinel-2 and Landsat-8 satellites, and daily weather forcing. The PROSAIL radiative transfer model is inversed in a first step to obtain Green Leaf Area Index (GLAI). The GLAI time series are then assimilated into the SAFYE-CO2 crop model taking into consideration their uncertainty. The chain is applied over winter wheat in the south-west of France during the cropping seasons 2017 and 2019. We compare the results against the net ecosystem exchange measured at the FR-AUR ICOS site (RMSE = 1.69 - 2.4 gC m−2 , R2 = 0.88 - 0.88), biomass (RMSE = 250 g m−2 , R2 = 0.9), and combine harvester yield maps. We quantify the difference between pixel and field and pixel scale simulations of biomass (bias = -47 g m−2 , -39 % variability), and the impact of the number of remote sensing acquisitions on the outputs (-66 % of mean uncertainty of biomass). Finally, we conduct a coherency analysis at regional scale to test the consistency of the observed patterns with soil texture, altitude and exposition variability. Results show higher biomass for higher clay soils and earlier emergence and senescence for south western exposition.