There is considerable interest in skewing the transmission of chirality, or 'handedness', from the molecular to the supramolecular level so that single-handed superstructures are created from mixed enantiomer systems. One approach is to flip the chirality of all the molecular building blocks to the same handedness. However, manipulation of molecular chirality is not possible for non-interconvertible enantiomers, and mechanisms that skew such systems are unclear. Here, we track the molecule-to-supramolecular chiral transfer in such systems at the nanoscale by probing molecular monolayers at surfaces. Scanning tunnelling microscopy and theoretical modelling show that enantiomeric imbalances lead to nonlinear symmetry breaking in organization, driven by configurational entropy effects. Thus, the majority enantiomer readily organizes into its superstructure with the minority left fragmented and disorganized, and thus impeded from realizing its superstructure. Such effects promise new strategies in chiral separations and enantioselective processes, and may have contributed to the homochiral evolution of complex matter from prebiotic environments.