This study synthesizes the budgets of three greenhouse gases (GHG, namely CO2, CH4, N2O) for Russia over two decades (2000–2009 and 2010–2019) using bottom-up and top-down approaches, as part of the Regional Carbon Cycle Assessment and Processes, Phase 2 (RECCAP2). Published estimates of natural sources and sinks of these GHGs in Russia vary widely. Here, bottom-up estimates are based on eddy covariance measurements, the Integrated Land Information System of Russia (ILIS-LEA), field data, Dynamic Global Vegetation Models (DGVMs), and regional models. The bottom-up approach estimated Net Ecosystem Exchange (NEE) at −0.64 ± 0.17 and −0.57 ± 0.14 Pg C yr−1, for decades 2000–2009 and 2010–2019, respectively. Top-down atmospheric inversions provide similar NEE carbon flux estimates with comparable uncertainties at −0.56 ± 0.26 and −0.73 ± 0.27 Pg C yr−1 for the two decades. Differences between these approaches arise from distinct flux components and structural assumptions. ILIS-LEA indicates a slightly declining carbon sink in 2010–2019, driven by increased disturbances. In contrast, DGVMs suggest a stable carbon sink over both decades but they do not fully simulate the effects of disturbances and recovery. Top-down inversions reveal an increasing CO2 sink, suggesting with additional observed constraints on biomass carbon increment that soil and non-forest biomes absorb more carbon than predicted by DGVMs and ILIS-LEA models. A Bayesian averaging approach estimates natural ecosystems acting as a GHG sink with a land-to-atmosphere flux of −1.55 ± 0.91 and −1.47 ± 0.82 Pg CO2-eq. yr−1. Accounting for both natural and anthropogenic emissions across the Russian territory shifts the net GHG balance to a source around 1.2 Pg CO2-eq. yr−1.