Over the last decade, the use of microalgae for biofuel production and carbon dioxide sequestration has become a challenge worldwide. Processing costs are still too high for these methods to be profitable though, leading to a need to find high value by-products to optimise the added value of this biomass. For high-throughput screening of such metabolites, it is essential to reach the inner content of the cell. This paper presents research and development of a technique enabling a high extraction yield of any metabolite, taking into account the difficulty of extracting bound and or inaccessible molecules with a wide variety of polarities. To this end, several disruption techniques were tested at laboratory scale on two biological models: Porphyridium purpureum and Phaeodactylum tricornutum. A mixer mill gave the best results, offering access to a broad diversity of metabolites from microalgae for high-throughput screening.