The aim of this study is to tailor the inner structure of positively charged poly-(N-isopropylacrylamid-co-allylamine) (P(NIPAM-co-AA)) microgels for a better control of the distribution of negatively charged magnetic cobaltferrite (CoFe2O4@CA) nanoparticles (MNPs) within the microgels. Therefore, two different strategies are followed for the microgel synthesis: the (one pot) batch method which leads to a higher cross-linker density in the microgel core and the feeding method which compensates different reaction kinetics of the cross-linker and the monomers. The latter one is expected to result in a homogeneous cross-linker distribution. Information about the cross-linker distribution is indirectly gained by measuring the elastic modulus via indentation experiments with an atomic force microscope. While the batch method results in a higher elastic modulus in the center of the microgel indicating a core/shell structure, the feeding method leads to a constant elastic modulus over the whole microgel. The loading with MNPs and their distribution are studied with transmission electron microscopy (TEM). The TEM images show a large difference in the MNP distribution which is correlated to the cross-linker distribution of both types of microgels. The batch method microgel has a low MNP concentration in the core. The feeding method microgel shows a much more homogeneous distribution of MNPs across the microgel. The latter one also shows a stronger charge reversal which is a hint for a higher loading of the feeding method microgel. Dynamic light scattering and electrophoretic mobility measurements demonstrate that for both types of microgels, the temperature sensitivity is preserved after loading with MNPs.