Gel-stabilized aqueous phases entrapping enzymes and surrounded by organic solvents have become promising tools for the biocatalytic conversion of hydrophobic compounds. In this work, we provide methods for an improvement of the solvent phase with special regard to the avoidance of gel agglomeration in batch as well as fluidized-bed reactors, and resulting effects on the catalyzed reaction. With alginate beads entrapping a lipase from Candida rugosa as investigation system, it was demonstrated that increasing the solvent polarity was only a limited measure to separate agglomerated beads, as water-unsaturated polar solvents extracted large amounts of water from the hydrogel. Water-saturated alcohols, however, were incorporated into side product esters by the entrapped enzyme. With non-polar solvents, like hexane, bead separation in batch reactors was achieved by the addition of certain surfactants to the organic phase. Best results were obtained with the cationic surfactant cetyl trimethyl ammonium chloride (CTAC), which in contrast to other surfactants only slightly affected the entrapped lipase and revealed no effects on the hydrogel structure. For the suspension of alginate beads in a fluidized-bed reactor, not only CTAC, but an additional increase in the solvent density was necessary, which affected the system’s productivity.