The preparation of small, monodispersed magnetic microparticles through microfluidic approaches has been consistently challenging due to the high energy input needed for droplet break-off at such small diameters. In this work, we show the microfluidic production of 1–3 μm magnetic nanoparticle-loaded poly(D, L-lactide) (PLA) microspheres. We describe the use of two approaches, using a conventional flow-focusing microfluidic geometry. The first approach is the separation of target size satellite particles from the main droplets; the second approach is the direct production using high flow rate jetting regimes. The particles were produced using a polymeric thiol-ene microfluidic chip platform, which affords the straightforward production of multiple chip copies for single-time use, due to large feature sizes and replica molding approaches. Through the encapsulation of magnetite/maghemite nanoparticles, and their characterization with scanning electron microscopy (SEM) and vibrating sample magnetometry (VSM) measurements, we show that the resulting particles are monosized, highly spherical and exhibit superparamagnetic properties. The particle size regime and their magnetic response show potential for in vivo intravenous applications of magnetic targeting with maximum magnetic response, but without blocking an organ's capillaries.