Algal symbiont-bearing benthic foraminifera are producers of both organic and inorganic carbon in coral-reef ecosystems. However, their contribution to the total budget of reef carbon production has not been adequately quantified. We used O2-respirometry and alkalinity-anomaly techniques to estimate the organic and inorganic carbon production rates of three species of symbiont-bearing large foraminifera common to coral reef flats in the northwest Pacific Ocean. The species studied were Baculogypsina sphaerulata and Calcarina gaudichaudii, which both harbor diatom endosymbionts, and Marginopora kudakajimensis, which harbors dinoflagellate endosymbionts. Live mature individuals were placed onto mesh in clear airtight containers filled with filtered seawater. The containers were incubated for several hours at a constant temperature and subjected to different levels of light intensity. Seawater was continuously mixed throughout the experiment. Dissolved oxygen, pH and total alkalinity were measured before and after incubation. Three species of larger benthic foraminifera were net organic and inorganic carbon producers. The P/R ratio exceeded 1 for all species. No photoinhibition was observed up to 1500 μmol photons m−2 s−1, and calcification was enhanced by light. These findings suggest that the three species are net carbon producers adapted to high-light, reef-flat environments. In addition, we calculated that Baculogypsina sphaerulata and C. gaudichaudii together accounted for 2–7.5% of the gross primary production of a reef-crest community, whereas M. kudakajimensis supplied 1–11% of the gross primary production of a backreef community. The two calcarinids and M. kudakajimensis contributed ~1 and 10% of the inorganic carbon production of seaward reef flat and protected lagoon communities, respectively. Together with previous reports, these estimates suggest that algal symbiont-bearing foraminifera play a minor but essential role in the organic and inorganic carbon production of coral-reef ecosystems.