The structural organization of iron oxide nanoparticles (NPs) obtained through in situ coprecipitation of iron salts in semi-interpenetrating polymer networks (semi-IPNs) constituted of alginate (Alg) and poly(N-isopropylacrylamide) (PNiPAAm) has been investigated by means of small-angle X-ray scattering and transmission electron microscopy. The oxidation reaction was repeated up to two times to increase the amount of iron oxide NPs formed. The results were compared to the synthesis of iron oxide nanoparticles in an alginate solution. It has been demonstrated that the polymeric gel acts as a spatial framework for iron oxide nanoparticles that controls their particle size distribution and that the application of repeating oxidation cycles does not increase the polydispersity of the iron oxide nanoparticles.