Contaminated soil organic matter from the Rocky Flats Environmental Technology Site (RFETS) has been previously shown to accumulate plutonium (Pu) in a colloidal subfraction and is hypothesized to contain cutin-like chemical structures cross-linked with hydroxamate functionality. The present study further characterizes this high Pu affinity subfraction using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) and discovers additional substructural components. The Pu-enriched fraction was extracted and purified through a series of ultrafiltration and isoelectric focusing (IEF) electrophoresis steps. Predominantly low H/C and high double-bond equivalence (DBE) aromatic and condensed aromatic molecular formulas were detected, 66% of which are included in a COO Kendrick mass defect (KMD) homologous series. This suggests the existence of polycarboxylated aromatic and condensed aromatic formulas, with CHON-type COO KMD formulas relatively more abundant in the purified subfraction where Pu had been observed than in the crude soil fractions which had successively lower Pu concentrations. Nitrogen contents increased with the progression of purification (bulk soil → crude colloid → IEF colloid) and coincided with the trend of Pu concentration; thus, we propose that these nitrogen and carboxyl functionalities of aromatic compounds may also impart significant Pu chelation character to the colloid.