This work is conceived to provide a reproducible and fast method to obtain optimal particle sizes for competitive ultrasoft magnetic applications based on Fe73.9Si15.5Cu1Nb3B6.6 nanostructured particles. In this scenario, partial nanocrystallization of the α-Fe3Si compound is promoted by annealing and subsequent high-energy ball milling processes. The milling is performed in this material, for the first time, by a combination of mixer, vibratory, and planetary ball milling motions. Under these conditions, structural and magnetic properties are tuned as a function of milling time with reduced particle size distributions and maintaining the ultrasoft magnetic character. In addition, drastic electronic and structural changes are observed after a few minutes of milling where the saturation magnetization and initial permeability are strongly influenced by the percentage of the α-Fe3Si nanocrystallites formed. Above 30 minutes of ball milling time, the formation of a low concentration of Nb2O5 clusters is detected by confocal Raman microscopy. This identification is essential since the rejection of the Nb from the amorphous matrix rich in Fe-Nb-B atoms acts as a marker of the seed mechanism that causes the deterioration of the softness character of these nanostructures. Therefore, on the one hand, this work introduces a successful procedure by combined milling processes to optimize the saturation magnetization and permeability with sub-micron particle sizes and, on the other hand, the detection of Nb2O5 clusters is implemented as an influential marker on the magnetic properties of these soft nanostructured particles.