Emission of greenhouse gases (GHGs) and removals from land, including both anthropogenic and natural fluxes, require reliable quantification, including estimates of uncertainties, to support credible mitigation action under the Paris Agreement. This study provides a state-of-the-art scientific overview of bottom-up anthropogenic emissions data from agriculture, forestry and other land use (AFOLU) in the European Union (EU281). The data integrate recent AFOLU emission inventories with ecosystem data and land carbon models and summarize GHG emissions and removals over the period 1990–2016. This compilation of bottom-up estimates of the AFOLU GHG emissions of European national greenhouse gas inventories (NGHGIs), with those of land carbon models and observation-based estimates of large-scale GHG fluxes, aims at improving the overall estimates of the GHG balance in Europe with respect to land GHG emissions and removals. Whenever available, we present uncertainties, its propagation and role in the comparison of different estimates. While NGHGI data for the EU28 provide consistent quantification of uncertainty following the established IPCC Guidelines, uncertainty in the estimates produced with other methods needs to account for both within model uncertainty and the spread from different model results. The largest inconsistencies between EU28 estimates are mainly due to different sources of data related to human activity, referred to here as activity data (AD) and methodologies (tiers) used for calculating emissions and removals from AFOLU sectors. The referenced datasets related to figures are visualized at https://doi.org/10.5281/zenodo.3662371 (Petrescu et al., 2020).