Developing potent drug molecules that are also highly soluble in aqueous media puts strong constraints on molecular design. As a result, there is intense interest today in developing drug formulation strategies that increase solubility. Specifically, nanosizing involves the reduction of the particle size of the active pharmaceutical ingredient (API) to the sub-micron range, which increases the surface area and dissolution rate. This strategy requires the addition of stabilizers, generally selected through extensive experimental screening, to maintain the desired physical properties over time. To better understand stabilization mechanisms and to develop better future formulations, atomic-level characterization of the particle structures is required in terms of both the size and spatial distribution of the components and the interactions. However, methods that can simultaneously provide this information are scarce. Here, using cinnarizine as a model for nanosuspensions, we show that by using DNP-enhanced NMR we can (i) detect and assign the API and the stabilizers present in formulations; (ii) observe atomic-level API-stabilizer interactions at natural isotopic abundance using two-dimensional 1H-13C correlation NMR experiments; and (iii) determine the domain sizes and the hierarchical structure of the API-stabilizer particles on the nano-meter length scale, based on polarization build-up curves and steady-state enhancements. We then use this approach to evaluate how freeze-drying and spray drying processes, generally used to isolate the material in the solid state, impact the particle structure. More broadly, the results confirm the applicability of DNP-enhanced NMR methods to characterize pharmaceutical suspensions or slurries, and to follow changes upon further processing.