Magnetic hybrid hydrogels have exhibited remarkable efficacy in various areas, particularly in the biomedical sciences, where these inventive substances exhibit intriguing prospects for controlled drug delivery, tissue engineering, magnetic separation, MRI contrast agents, hyperthermia, and thermal ablation. Additionally, droplet-based microfluidic technology enables the fabrication of microgels possessing monodisperse characteristics and controlled morphological shapes. Here, alginate microgels containing citrated magnetic nanoparticles (MNPs) were produced by a microfluidic flow-focusing system. Superparamagnetic magnetite nanoparticles with an average size of 29.1 ± 2.5 nm and saturation magnetization of 66.92 emu/g were synthesized via the co-precipitation method. The hydrodynamic size of MNPs was changed from 142 nm to 826.7 nm after the citrate group’s attachment led to an increase in dispersion and the stability of the aqueous phase. A microfluidic flow-focusing chip was designed, and the mold was 3D printed by stereo lithographic technology. Depending on inlet fluid rates, monodisperse and polydisperse microgels in the range of 20–120 μm were produced. Different conditions of droplet generation in the microfluidic device (break-up) were discussed considering the model of rate-of-flow-controlled-breakup (squeezing). Practically, this study indicates guidelines for generating droplets with a predetermined size and polydispersity from liquids with well-defined macroscopic properties, utilizing a microfluidic flow-focusing device (MFFD). Fourier transform infrared spectrometer (FT-IR) results indicated a chemical attachment of citrate groups on MNPs and the existence of MNPs in the hydrogels. Magnetic hydrogel proliferation assay after 72 h showed a better rate of cell growth in comparison to the control group (p= 0.042).