Phytoplankton harvests light by integrating chlorophyll in protein-pigment complexes (photosystems) that are variable in number and size. In ecosystem models, the capacity of light harvesting is described as the pool of chlorophyll. Since most of the variability in phytoplankton chlorophyll content is driven by acclimation to changing nutrient and light conditions, photoacclimation is generally parameterized as a regulation of chlorophyll synthesis with changing light. However, photosystems can also be degraded, and of the few process-based models that have been proposed in the literature for the representation of their degradation and repair, none of them have been extended to more realistic conditions offered by pelagic biogeochemical models. We proposed three potential parameterizations to treat the degradation of photosystems as a function of light intensity and included them as a source of variation in the size of the chlorophyll pool in Regulated Ecosystem Model, version 2 (REcoM2). These model versions provided chlorophyll values highly correlated with satellite chlorophyll and accurate patterns of the chlorophyll to carbon ratio at global scale. The improvement in the prediction of the ratios was remarkable in scenarios where cells are exposed to periods of low light conditions. By isolating the effects of light and nutrients on the variability of the chlorophyll to carbon ratio and the growth rate, we observed a potential reduction in photosynthetic performance under simultaneous light saturation and nutrient stress. This effect, whose strength depends on the presence of photoprotective mechanisms and the degree of nutrient limitation, allowed to assess the role of photodamage and photoprotection under stress conditions.