Transition-metal dichalcogenides (TMDs) intercalated with magnetic ions serve as a promising materials platform for developing next-generation, spin-based electronic technologies. In these materials, one can access a rich magnetic phase space depending on the choice of intercalant, host lattice, and relative stoichiometry. The distribution of these intercalant ions across given crystals, however, is less well defined-particularly away from ideal packing stoichiometries-and a convenient probe to assess potential longer-range ordering of intercalants is lacking. Here, we demonstrate that confocal Raman spectroscopy is a powerful tool for mapping the onset of intercalant superlattice formation in Fe-intercalated NbSe2 (FexNbSe2) for 0.14 ≤ x < 0.25. We use single-crystal X-ray diffraction to confirm the presence of longer-range intercalant superstructure and employ polarization-, temperature-, and magnetic field-dependent Raman measurements to examine both the symmetry of emergent phonon modes in the intercalated material and potential magnetoelastic coupling. Magnetometry measurements further indicate a correlation between the onset of magnetic ordering and the relative degree of intercalant superlattice formation. These results show Raman spectroscopy to be an expedient, local probe for mapping intercalant ordering in this class of magnetic materials.