The application range of man-made cellulosic fibers is limited by the absence of cost- and manufacturing-efficient strategies for anisotropic hierarchical functionalization. Overcoming these bottlenecks is therefore pivotal in the pursuit of a future bio-based economy. Here, we demonstrate that colloidal silica nanoparticles (NPs), which are cheap, biocompatible and easy to chemically modify, enable the control of the cross-sectional morphology and surface topography of ionic liquid-spun cellulose fibers. These properties are tailored by the silica NPs' surface chemistry and their entry point during the wet-spinning process (dope solution ^DSiO₂ or coagulation bath ^CSiO₂). For ^CSiO₂-modified fibers, the coagulation mitigator dimethylsulphoxide allows for controlling the surface topography and the amalgamation of the silica NPs into the fiber matrix. For dope-modified fibers, we hypothesize that cellulose chains act as seeds for directed silica NP self-assembly. This results for ^DSiO₂ in discrete micron-sized rods, homogeneously distributed throughout the fiber and for glycidoxy-surface modified ^DSiO₂@GLYEO in nano-sized surface aggregates and a cross-sectional core-shell fiber morphology. Furthermore, the dope-modified fibers display outstanding strength and toughness, which are both characteristic features of biological biocomposites.