This dataset is a synthesis of terrestrial and freshwater CO2 and CH4 fluxes from the Arctic-Boreal region aggregated to monthly timesteps. The dataset, known as ABCFlux v2, includes 1,028 unique sites and spans 1984-2024 with the majority of observations occurring after 1999. ABCFlux v2 includes surface-atmosphere CO2 fluxes of net ecosystem exchange (NEE), gross primary production (GPP), and ecosystem respiration (Reco) alongside CH4 fluxes. For aquatic ecosystems, CH4 fluxes were split into diffusive and ebullitive flux pathways and included potential emissions from transient storage in the water column, alongside CO2 and CH4 concentrations dissolved in the surface water. Fluxes were measured through a variety of methods including chamber and eddy covariance techniques alongside bubble traps, ice-surveys, and concentration-based turbulence-driven modelling in aquatic ecosystems. Supporting variables include methodological metadata (e.g., gap-filling methods, number of chamber measurement days), environmental measurements (e.g., air, water, and soil temperatures), and site-level attributes (e.g., permafrost thaw status, disturbance history). Compared with version 1, this v2 dataset includes additional variables to represent detailed descriptions of plant functional types, deep soil temperatures (<10 cm), and permafrost thaw presence or absence in the top two meters. Data pertaining to CH4 fluxes were also added that were not included in previous version. The data are provided in comma separated values (CSV) format.