In this study, we compared the GR51PP (hydrophobic/polysulfone) membrane with a series of hydrophilic (regenerated cellulose) membranes with the aim of increasing the retention of products and decreasing membrane fouling. The raw material used was a sodium-based spent sulfite liquor from the sulfite pulping process of spruce and pine. The results show that the hydrophilic membranes were superior to the hydrophobic membranes in terms of higher fluxes (up to twice the magnitude), higher product retentions and less fouling (up to five times lower fouling). The fouling was probably caused by pore blocking as observed in earlier studies. However, the hydrophilic membranes had a lower affinity for lignin, which was indicated by the lower retention and fouling. This also resulted in a separation degree, which was higher compared with the hydrophobic membrane, thus yielding a higher galactoglucomannan (GGM) purity. 2D HSQC NMR results show that no major structural differences were present in the hydrophilic and hydrophobic retentates. A techno-economical evaluation resulted in the RC70PP being chosen as the most cost-efficient membrane in terms of flux and product recovery.