The use of biopolymers obtained from natural resources as a carbon source has attracted much attention. In this study, we introduced a novel method for synthesis of hollow magnetic carbon microbeads (HMCMs) based on core-shell alginate hydrogel microbeads consisting of a hydrophobic iron-oleate core encapsulated in a shell of ionically cross-linked alginate hydrogel using the syringe pump with the fabricated double-layered syringe needle. This allows in-situ formation of magnetic particles and carbon walls simultaneously during carbonization. After surface passivation with a silica coating followed by direct carbonization led to in-situ formation of iron oxide particles via the thermal decomposition of the iron-oleate precursor in the core region and a carbon shell derived from the cross-linked alginate polymer during carbonization. The subsequent removal of the silica shell resulted in the formation of HMCMs with a unique surface wrinkle morphology and superparamagnetic property. HMCMs were applied to remove dye from the contaminated wastewater, and the dye-adsorbed HMCMs could be easily removed by an external magnetic field. The proposed synthesis of hollow carbon microbeads can be further optimized to control the size of core-shell microbeads and the components encapsulated in the core and shell, and hence will be useful for preparing diverse types of beads for various applications.