•Magnetic nanogels self-assemble in zero field.•There are three length scales in magnetic nanogel structure factors.•Self-assembly of magnetic nanogels happens if magnetic interactions are strong. Magnetic nanogels represent a cutting edge of magnetic soft matter research due to their numerous potential applications. Here, using Langevin dynamics simulations, we analyse the influence of magnetic nanogel concentration and embedded magnetic particle interactions on the self-assembly of magnetic nanogels at zero field. For this, we calculated radial distribution functions and structure factors for nanogels and magnetic particles within them. We found that, in comparison to suspensions of free magnetic nanoparticles, where the self-assembly is already observed if the interparticle interaction strength exceeds the thermal fluctuations by approximately a factor of three, self-assembly of magnetic nanogels only takes place by increasing such ratio above six. This magnetic nanogel self-assembly is realised by means of favourable close contacts between magnetic nanoparticles from different nanogels. It turns out that for high values of interparticle interactions, corresponding to the formation of internal rings in isolated nanogels, in their suspensions larger magnetic particle clusters with lower elastic penalty can be formed by involving different nanogels. Finally, we show that when the self-assembly of these nanogels takes place, it has a drastic effect on the structural properties even if the volume fraction of magnetic nanoparticles is low.