Colloid aggregation and retention in the presence of macromolecular coatings (e.g., adsorbed polymers, surfactants, proteins, biological exudates, and humic materials) have previously been correlated with electric double layer interactions or repulsive steric interactions, but the underlying causes are not fully resolved. An interaction energy model that accounts for double layer, van der Waals, Born, and steric interactions as well as nanoscale roughness and charge heterogeneity on both surfaces was extended, and theoretical calculations were conducted to address this gap in knowledge. Macromolecular coatings may produce steric interactions in the model, but non-uniform or incomplete surface coverage may also create compressible nanoscale roughness with a charge that is different from the underlying surface. Model results reveal that compressible nanoscale roughness reduces the energy barrier height and the magnitude of the primary minimum at separation distances exterior to the adsorbed organic layer. The depth of the primary minimum initially alters (e.g., increases or decreases) at separation distances smaller than the adsorbed organic coating because of a decrease in the compressible roughness height and an increase in the roughness fraction. However, further decreases in the separation distance create strong steric repulsion that dominates the interaction energy profile and limits the colloid approach distance. Consequently, adsorbed organic coatings on colloids can create shallow primary minimum interactions adjacent to organic coatings that can explain enhanced stability and limited amounts of aggregation and retention that have commonly been observed. The approach outlined in this manuscript provides an improved tool that can be used to design adsorbed organic coatings for specific colloid applications or interpret experimental observations.