Biominerals are composite materials with inorganic and organic components. The latter provide insights into how organisms control mineralization and, if derived from micro/nannofossils, into past climates. Many calcifying organisms cannot be cultured or are extinct; the only materials available for their study are therefore complex environmental samples in which the organism of interest may only be a minor component. There is currently no method for characterizing the biomineral-associated organic material from single particles within such assemblages, so its compositional diversity is unknown. Focusing on coccoliths, we demonstrate that surface-enhanced Raman scattering microspectroscopy can be used to determine the origin and composition of fossil organic matter at the single-particle level in a heterogeneous micro/nannofossil assemblage. This approach may find applications in the study of micro/nannofossil assemblages and uncultivated species, providing evolutionary insights into the macromolecular repertoire involved in biomineralization.