These datasets contain measurements from BGC-Argo floats equipped with a transmissometer and which cover the Southern Ocean from 2014 to 2019. The first dataset ("profile_data.csv") includes bio-optical profiles of the particulate backscattering coefficient (BBP in m-1), the concentration of Chlorophyll-a (CHLA in mg m-3), and the particulate beam attenuation coefficient (CP in m-1) with data processing and quality control described in the manuscript entitled “BioGeoChemical-Argo floats reveal stark latitudinal gradient in the Southern Ocean deep carbon flux driven by phytoplankton community composition” submitted to Global Biogeochemical Cycles. In the second file (i.e. "flux_1000m.csv"), we provided attenuance fluxes (in day-1) at 1000m measured by the transmissometer acting as an Optical Sediment Trap. These flux values were then converted to POC fluxes (mg POC m-2 day-1) with the method described in the submitted manuscript.