Versatile methods are here presented for the assembling of magnetic nanoparticles in controlled super-structures with different final aspect ratios. The first step of the procedure is based on the destabilization, and consequently clustering, of a dextran-coated nanoparticles suspension, altering the colloidal stability of the initial building blocks. Subsequently, a second polysaccharide shell, based on chitosan, is grafted to the super-structure surface, for stopping the aggregation of the nanoparticles and enhancing the stability of the resulting assembly. For achieving a finer control of the process, spherical magnetic clusters (SMC) are prepared through a microfluidic aided clustering, investigating the contribution of flow rates and injection scheme geometry to the nanoparticle assembly. Besides, the use of static magnetic fields applied during the first step results in the preparation of micrometric elongated magnetic super-structures (EMS), tuning the average aspect ratio up to a value of 13±4.