Tetraselmis is an interesting microalga for food products because of its high protein content and surface productivity as well as the possibility to scale up the culture easily. However, this specie is yet understudied compared to other algae such as Chlorella. Different batches of Tetraselmis chui were received from the same supplier, with different morphological properties, probably associated with a difference in physiological state: one batch contained circular and dividing cells and the other flagellated cells. The batches were characterized biochemically in terms of protein, carbohydrate and ash content and the rupturability was tested to characterize their behavior to cell disruption. One batch was found way more fragile than the other. The bead milling of the two batches showed also striking differences in terms of cell disruption kinetic, as well as dry matter repartition after centrifugation and protein recovery yields within the supernatant. Nearly no differences in protein yield were observed after bead milling in comparison to freeze-thawing for the resistant batch, with a final yield of 11 % of the initial proteins. However, a clear protein release was observed for the fragile batch along the milling residence time, with a final protein yield of 32 %. The protein released were characterized by SDS PAGE and zymography and differences were observed, confirming the difference in metabolism. Several physicochemical modifications were applied to the cell lysate to increase the yields using pH, temperature and dilution. This latest modification was the most promising. The results underlined that a difference in physiological state of Tetraselmis chui had a significant impact on the following biorefinery, affecting directly the cell disruption and the protein recovery yields. The valorization of the whole microalgae thus necessitates the finest coupling between upstream and downstream.