This paper presents a mathematical model capable of quantitative prediction of the state of the photo-synthetic apparatus of microalgae in terms of their open, closed and damaged reaction centers undervariable light conditions. This model combines the processes of photoproduction and photoinhibition inthe Han model with a novel mathematical representation of photoprotective mechanisms, including qE-quenching and qI-quenching. For calibration and validation purposes, the model can be used to simulatefluorescence fluxes, such as those measured in PAM fluorometry, as well as classical fluorescence indexes.A calibration is carried out for the microalga Nannochloropsis gaditana, whereby 9 out of the 13 modelparameters are estimated with good statistical significance using the realized, minimal and maximal flu-orescence fluxes measured from a typical PAM protocol. The model is further validated by considering amore challenging PAM protocol alternating periods of intense light and dark, showing a good ability toprovide quantitative predictions of the fluorescence fluxes even though it was calibrated for a differentand somewhat simpler PAM protocol. A promising application of the model is for the prediction of PI-response curves based on PAM fluorometry, together with the long-term prospect of combining it withhydrodynamic and light attenuation models for high-fidelity simulation and optimization of full-scalemicroalgae production systems.