The remineralisation of sinking particles by prokaryotic heterotrophic activities is important for controlling oceanic carbon sequestration. Here, we report mesopelagic particulate organic carbon (POC) remineralisation fluxes in the North Atlantic along the GEOTRACES-GA01 section (GEOVIDE cruise; May–June 2014) using the particulate biogenic barium (excess barium; Baxs) proxy. Important mesopelagic (100–1000 m) Baxs differences were observed along the transect depending on the intensity of past blooms, the phytoplankton community structure and the physical forcing, including downwelling. The subpolar province was characterized by the highest mesopelagic Baxs content (up to 727 pmol L−1), which was attributed to an intense bloom averaging 6 mg Chl-a m−3 between January and June 2014 and by an intense 1500 m-deep convection in the central Labrador Sea during the winter preceding the sampling. This downwelling could have promoted a deepening of the prokaryotic heterotrophic activity, increasing the Baxs content. In comparison, the temperate province, characterized by the lowest Baxs content (391 pmol L−1), was sampled during the bloom period and phytoplankton appear to be dominated by small and calcifying species, such as coccolithophorids. The Baxs content, related to an oxygen consumption, was converted into a remineralisation flux using an updated relationship, proposed for the first time in the North Atlantic. The estimated fluxes were in the same order of magnitude than other fluxes obtained by independent methods (moored sediment traps, incubations) in the North Atlantic. Interestingly, in the subpolar and subtropical provinces, mesopelagic POC remineralisation fluxes (up to 13 and 4.6 mmol C m−2 d−1, respectively) were equalling and occasionally even exceeding upper ocean POC export fluxes, highlighting the important impact of the mesopelagic remineralisation on the biological carbon pump with a near-zero, deep (> 1000 m) carbon sequestration efficiency in spring 2014.