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Abstract A warmer ocean will change plankton physiological rates, alter plankton community composition, and in turn affect ecosystem functions, such as primary production, recycling, and carbon export. To predict how temperature changes affect plankton community dynamics and function, we developed a mechanistic trait‐based model of unicellular plankton (auto‐hetero‐mixotrophic protists and bacteria). Temperature dependencies are specifically implemented on cellular process rather than at the species level. As the uptake of resources and metabolic processes have different temperature dependencies, changes in the thermal environment will favor organisms with different investments in processes such as photosynthesis and biosynthesis. The precise level of investments, however, is conditional on the limiting process and is ultimately determined dynamically by competition and predation within the emergent community of the water column. We show how an increase in temperature can intensify nutrient limitation by altering organisms' interactions, and reduce relative cell‐size in the community. Further, we anticipate that a combination of temperature and resource limitation reduces ecosystem efficiency at capturing carbon due to strengthening of the microbial loop. By explicitly representing the effects of temperature on traits responsible for growth, we demonstrate how changes on the individual level can be scaled up to trends at the ecosystem level, helping to discern direct from indirect effects of temperature on natural plankton communities.