Microzooplankton ingest a significant fraction of primary production in the ocean and thus remineralize nutrients and stimulate regenerated primary production. We synthesized observations on microzooplankton carbon-specific grazing rate, partitioning of grazed material, respiration rate, microzooplankton biomass, microzooplankton-mediated phytoplankton mortality rate, and phytoplankton growth rate. We used these observations to parameterize and evaluate the microzooplankton compartment in a global biogeochemical model that represents five plankton functional types. Microzooplankton biomasses predicted in this simulation are closer to the independently derived evaluation data than in the previous model version. Most rates, including primary production, microzooplankton grazing, and export of sinking detritus are within observational constraints. However, the model underestimates microzooplankton and mesozooplankton biomasses and chlorophyll concentrations. Thus, we propose that sufficient carbon enters the model ecosystem, but insufficient carbon is retained. For microzooplankton, the low retention of carbon could be improved by parameterizing the model with ciliate gross growth efficiency only, indicating that ciliates may contribute more to microzooplankton activity than their biomass contribution suggests. By taking into account the model underestimation of biomass, we estimate that the ocean inventory of microzooplankton biomass is 0.24 Pg C (a range of 0.14–0.33 Pg C), which is similar to the biomass of mesozooplankton.