Assemblies of carbohydrate polymers are important in a number of applications and improved methods for their fabrication are increasingly sought after. Herein, we report that an aqueous two-phase system of alginate (Alg) and hydroxypropyl cellulose with poly(methacrylic acid) graft chains (HPC-PMA) facilitated the assembly of Alg/HPC-PMA in both phases. Dynamically formed filamentous domains in a flow field were gelled by rapid complexation with cationic polyethyleneimine (PEI). The fabricated HPC-PMA gel filament morphologies can be switched between the bundled and dissociated gel filaments using a co-flow microfluidic device in response to the amount of supplied PEI crosslinker. Excess complexation of PEI contributes to the fabrication of cationic gel filaments; this contribution results in a dissociated structure due to electrostatic repulsion. In contrast, an appropriate amount of PEI resulted in a bundle structure. The proposed spinning method avoids the risk of nozzle clogging, and enables the one-step spinning of multiple gel filaments.