Soft magnetic metal amorphous nanocomposite alloys are produced through rapid solidification and thermal annealing yielding nanocrystals embedded within an amorphous precursor. Similar free energies in Co-rich and FeNi-based alloy systems result in multiple nanocrystalline phases being formed during devitrification. Studies of multi-phase crystallization processes have been reported for Co-rich alloys but relatively few have investigated FeNi-based systems. A detailed characterization of compositional partitioning and microstructure of an optimally annealed FeNi-based MANC (Fe70Ni30)80Nb4Si2B14 alloy is presented through complementary high-resolution transmission electron microscopy (HRTEM) and atom probe tomography (APT). HRTEM demonstrates orientation relationships between FCC and BCC nanocrystals, suggesting heterogeneous nucleation of nanocrystals in the amorphous matrix or a cooperative mechanism of nucleation between BCC and FCC nanocrystallites. APT results show evidence for (i) the segregation of Fe and Ni between nanocrystals of different phases, (ii) B partitioning to the amorphous phase, and (iii) an Nb-enriched shell surrounding nanocrystals.