The structure of aqueous propylamine mixtures is investigated through X-ray and neutron scattering experiments, and the scattered intensities compared with computer simulation data. Both sets of data show a prominent scattering pre-peak, which first appears at propylamine mole fraction x ≥ 0.1 around scattering vector k ≈ 0.2 Å−1, and evolves towards k ≈ 0.8 Å−1 for neat propylamine x = 1. The existence of a scattering pre-peak in this mixture is unexpected, specifically in view of its absence in aqueous 1-propanol or aqueous DMSO mixtures. The detailed analysis of the various atom–atom structure factors and snapshots indicates that significant micro-structures exist, which produces correlation pre-peaks in the atom–atom structure factors, positive for like species atom correlations and negative for cross species correlations. The scattering pre-peak depends on how these two contributions cancel out or not. The way the amine group bonds with water produces a pre-peak through an imbalance of the positive and negative scattering contributions, unlike 1-propanol and DMSO, where these 2 contributions compensate exactly. Hence molecular simulations demonstrate how chemical details influence the microscopic segregation in different types of molecular emulsions and can be detected or not by scattering experiments.