Superparamagnetic iron oxide nanoparticles (SPIONs) have attracted significant attention because of their nanoscale magnetic properties. SPION aggregates may afford emergent properties, resulting from dipole-dipole interactions between neighbors. Such aggregates can display internal order, with high packing fractions (>20%), and can be stabilized with block co-polymers (BCPs), permitting design of tunable composites for potential nanomedicine, data storage, and electronic sensing applications. Despite the routine use of magnetic fields for aggregate actuation, the impact of those fields on polymer structure, SPION ordering, and magnetic properties is not fully understood. Here, we report that external magnetic fields can induce ordering in SPION aggregates that affect their structure, inter-SPION distance, magnetic properties, and composite Tg. SPION aggregates were synthesized in the presence or absence of magnetic fields or exposed to magnetic fields post-synthesis. They were characterized using transmission electron microscopy (TEM), small angle X-ray scattering (SAXS), superconducting quantum interference device (SQUID) analysis, and differential scanning calorimetry (DSC). SPION aggregate properties depended on the timing of field application. Magnetic field application during synthesis encouraged preservation of SPION chain aggregates stabilized by polymer coatings even after removal of the field, whereas post synthesis application triggered subtle internal reordering, as indicated by increased blocking temperature (TB), that was not observed via SAXS or TEM. These results suggest that magnetic fields are a simple, yet powerful tool to tailor the structure, ordering, and magnetic properties of polymer-stabilized SPION nanocomposites.