Microalgae can provide a more sustainable alternative to traditional food systems which are dominated by terrestrial crops. The main economic challenges, however, relate to the downstream processing of microalgae and the valorization of their side streams. The present work explores the scientific principles and data required to develop an integrated biorefinery-on-a-chip, which replaces many of the common downstream processing unit operations by employing acoustic fields. The acoustic parameters of Tisochrysis lutea microalgal cells and their cell components are determined using the neutrally buoyant state method. Culture conditions which result in a high carbohydrate or high protein to lipid ratio led to a higher acoustic contrast factor than culture conditions favoring a high composition of lipids. The collected acoustic data is used as input in a numerical model which studies the harvesting of microalgal cells and the fractionation of microalgal cell components. High separation levels are achieved based on the size and composition of microalgal cells and the type of cell component. Subsequent studies are envisioned to determine the practical feasibility of applying these concepts and even scaling them out. Nevertheless, this study represents a steppingstone towards a novel, label-free approach to processing microalgal cells of different biomass compositions.