In this study, we present a new synthesis methodology based on photo-crosslinking-assisted continuous precipitation polymerization which allows controlling the distribution of crosslinks in microgels. In our approach we substituted conventional crosslinking agent by a comonomer carrying photo-crosslinkable 4-oxocyclopent-2-en-1-yl group. Microgel size, morphology, distribution of crosslinks and packing density of the polymer chains are studied as a function of retention time (Rt) in the flow reactor. Dynamic and static light scattering (DLS and SLS) as well as small angle X-ray scattering (SAXS) proved an excellent level of control over the distribution of crosslinks in microgels during the polymerization process. These results were confirmed by atomic force microscopy (AFM), indicating a difference in microgel stiffness and arrangement of the polymer network as resulting from increased Rt.