The optimization of cell disruption is a critical step in microalgal biorefineries. We used the same batch of Tetraselmis suecica culture to compare two mechanical cell disruption techniques, focusing on the extraction yield of water-soluble molecules. The conditions for high-pressure homogenization (HPH) studied were two passes at a moderate pressure of 300 bars. For ultrasound (US) treatment, we used an amplitude of 20% (equivalent to 100 W) for 25 min. These conditions were chosen on the basis of a preliminary screen of extraction conditions. HPH extracted proteins and pigments more efficiently than US, whereas US was superior for uronic acid extraction. Interestingly, the two methods had similar extraction yields for carbohydrates under the studied conditions. We also analyzed the kinetics of molecule release by considering the centrifugation time lag for HPH and applying a first-order kinetic model for US. HPH outperformed US in terms of the immediate extraction and release of molecules.