Assessing the carbon footprint of marine bivalve aquaculture demands an accurate estimation of the CO2 release associated to capital goods and aquaculture operations but also to the metabolic CO2 budget of the cultured species. Nowadays, there are discrepancies on the processes to include in that budget, how to estimate them, and which scale should be applied, from individual to ecosystem. Site-specific environmental conditions and culture methods also affect significantly the estimates. Here, we have gathered environmental, biochemical and metabolic data from published scientific articles, reports and existing databases to present the metabolic CO2 budget for mussel aquaculture in the coastal inlets of the Northwest Iberian upwelling. We analyse the contribution of mussel flesh and shell production jointly and separately. At the individual scale, the shell CO2 budget is estimated from CO2 removal by shell matrix protein synthesis and CO2 release during calcification and respiration to support shell maintenance. Organic carbon in mussel flesh and CO2 released by respiration to support flesh maintenance contribute to the flesh CO2 budget. Only calcification and respiration processes are considered when estimating the metabolic carbon footprint of individual mussels because organic carbon in mussel flesh and shell returns to the atmosphere as CO2 in a relatively short period. While the metabolic carbon footprint associated to mussel shell remains constant at 365 kg CO2 per ton of shell, it varies from 92 to 578 kg CO2 per ton of mussel flesh. This large variability depends on mussel seeding time and harvesting size, due to the differential seasonal growth patterns of flesh and shell. Inclusion of the CO2 potentially immobilised in mussel faeces buried in the sediments would lead to a reduction of the metabolic carbon footprint estimates by up to 6 % compared with the individual estimates.