Photosynthesis by phytoplankton in sunlit surface waters transforms inorganic carbon and nutrients into organic matter, a portion of which is subsequently transported vertically through the water column by the process known as the biological carbon pump (BCP). The BCP sustains the steep vertical gradient in total dissolved carbon, thereby contributing to net carbon sequestration. Any changes in the vertical transportation of the organic matter as a result of future climate variations will directly affect surface ocean carbon dioxide (CO2) concentrations, and subsequently influence oceanic uptake of atmospheric CO2 and climate. Here we present results of experiments designed to investigate the potential effects of ocean acidification and warming on the BCP. These perturbation experiments were carried out in enclosures (3,000 L volume) in a controlled mesocosm facility that mimicked future pCO2 (∼900 ppmv) and temperature (3°C higher than ambient) conditions. The elevated CO2 and temperature treatments disproportionately enhanced the ratio of dissolved organic carbon (DOC) production to particulate organic carbon (POC) production, whereas the total organic carbon (TOC) production remained relatively constant under all conditions tested. A greater partitioning of organic carbon into the DOC pool indicated a shift in the organic carbon flow from the particulate to dissolved forms, which may affect the major pathways involved in organic carbon export and sequestration under future ocean conditions.