We have improved the AqSO biorefinery by increasing its resource efficiency and by optimizing properties of the extracted lignin for valorization applications. We accomplished this by using BO to construct surrogate models capable of predicting experimental targets (lignin yield and moieties quantified using 2D NMR) in terms of the processing conditions (temperature, P-factor). Using the depolymerization of lignin into platform chemicals as an example application, we subsequently applied a Pareto front analysis to determine the processing conditions that provide optimal balance between high lignin yield and high amount of β-O-4 linkages. The derived processing conditions thus allows for resource efficient extraction of β-O-4-rich lignin suitable for depolymerization applications.