Magnetic nanoparticles find widespread attention with numerous applications, such as in nanomedicine or catalysis through the magnetic heating effect, in smart fluids, and active matter with self-propelling particles that can be manipulated with static and dynamic magnetic fields. Whereas the implementation of nanomagnetic properties into technological applications is progressing rapidly, fundamental questions remain challenging, such as the evolution of nanoscale magnetization and magnetization relaxation or the microscopic interaction between nanoscale magnetic units. Our approach to such questions lies in the cross-scale investigation of structure and magnetization in nanostructured materials using a combination of X-ray and polarized neutron scattering. In this talk I will give insight into the nanoscale distribution of magnetic order and disorder within nanoparticles. Being intrinsic to nanomaterials, disorder effects crucially determine the magnetization properties of magnetic nanoparticles. I will further present our work on self-organization of nanoparticles into regular arrangements and the arising magnetic coupling phenomena.