Commercial application of biocatalysts depends on the efficiency of the immobilization method and residual enzyme activity. Electrospinning offers a simple and versatile route to immobilize enzymes in submicron-sized fibers and thus improved mass transfer characteristics. Performance of encapsulation of fructosyltransferase from Bacillus subtilis by emulsion, suspension, and coaxial electrospinning was compared. We particularly focused on the effect of hydrophilic properties of a set of biodegradable polymers on support's activity. Bioactivity of electrospun support in aqueous medium increased in order of the matrix hydrophilicity. Additionally, the efficiency of electrospun fibers was compared with SepabeadsA (R), commercial epoxy-activated resins. In fibers, enzyme loading of 68.1 mg/g and specific enzyme activity of 5.5 U/mg was achieved compared to 49.5 mg/g and 2.2 U/mg on Sepabeads. Fructosyltransferase exhibited high sensitivity towards organic solvents and covalent attachment, respectively. Immobilization of native enzyme in coaxial fibers increased the specific activity to approx. 30 U/mg which corresponds to 24% of that of the free enzyme. Finally, operational stability of fiber supports was examined in a plug-flow reactor and 5% of initial substrate conversion remained after > 2000 cycles. The efficiency of core-shell immobilizates compared to one-dimensional fibers was both in batch and continuous reaction at least 4.4-fold higher.