A microfluidic platform for continuous synthesis of hydrogel microparticles with superparamagnetic colloids (SPCs) embedded at prescribed positions is described. The shape of the cross-linked microparticle is independently controlled by stop–flow lithography, whereas the position of trapped SPCs are dictated by virtual magnetic moulds made of 2D nickel patches facilitating magnetic trapping. The spatial positions of trapped SPCs collectively function as a binary code matrix for product authentication. Analytical and finite element methods are combined to optimize the trapping efficiency of SPCs by systematically investigating magnetic field microgradients produced by nickel patches. It is envisioned that the proposed magnetic microparticles will contribute to the development of soft matter inspired product quality control, tracking and anti-counterfeiting technologies.