This study evaluates the performance of a flaxseed-derived bioflocculant for solid–liquid separation in mineral processing, focusing on phosphate concentrate and phosphate sludge. A Design of Experiments (DoE) approach was employed to optimize a simple and scalable aqueous extraction process by assessing the effects of key parameters, including extraction temperature, seed loading, agitation speed, residence time, NaCl concentration, and dilution injection mode. The results demonstrate that a single optimized extraction condition yields an effective bioflocculant suitable for both phosphate matrices. Among the studied factors, seed loading, extraction temperature, agitation speed, residence time, and dilution injection mode were identified as the most influential variables affecting extraction yield and flocculation efficiency. The predictive models exhibited excellent accuracy (R² > 99%), confirming the robustness of the optimization strategy. Sedimentation tests showed a marked improvement in settling kinetics in both matrices, with performance comparable to conventional polyacrylamide-based flocculants. Optimal dosages were approximately 400 g/t for phosphate concentrate and 205 g/t for phosphate sludge. An injection concentration of 0.5 g/L was found to provide an optimal balance between flocculation efficiency and water usage. Chemical characterization revealed a complex composition of organic acids, phenolic compounds, flavonoids, and lignans. Zeta potential measurements indicated that both particles and bioflocculant remained negatively charged, suggesting that flocculation is governed primarily by a polymer bridging mechanism, supported by hydrogen bonding interactions. Overall, flaxseed-derived bioflocculants represent a sustainable and efficient alternative for mineral processing and water recovery applications.