Microalgae possess a cell wall with remarkable physical and chemical strength, which has proved to be a bottleneck for extraction techniques. With the application of spark discharges instigated by 100-ns high voltage pulses, a novel method was established that was found to be effective and yet gentle for the extraction of sensitive, especially heat-sensitive, compounds. The spark, which was ignited directly in the submerged algae suspension, is characterised by several physical and chemical processes that might promote a successful disintegration of the cells. Among other characteristics, the conceivably most destructive mechanism, i.e. strong shockwaves, was examined with schlieren diagnostics to evaluate associated pressures. The results were compared with the tensile strength, determined by atomic force microscopy, of Chlorella vulgaris, which was chosen as model organism. A shockwave pressure of 500 MPa in the close vicinity of the discharge by far exceeded the elasticity modulus of the algae with 13.95 MPa, confirming the potential of mechanically breaking the cell wall. At the same time, bulk temperatures could be maintained close to room temperature by adjusting the operating parameters for the spark-application, hence, especially encouraging the extraction of thermally unstable intracellular substances.