Bis-ureas are generally associated with strongly bifurcated hydrogen bonds (NH···OC interactions). For this reason, a series of trisubstituted bis-ureas (TBU) with bulk substituents were designed and used as a study model to gain a better understanding of the persistence of NH···OC interactions as driving interactions of the crystallization process. The TBU molecules possess different substituents (isopropyl, benzyl, and 4-nitro-benzyl) and variations in the methylene spacer. The TBU self-assembly, through crystallization mechanism proposals, is discussed related to the role of intermolecular interactions that drive and participate in the crystallization process. The intermolecular interactions present in the proposed first nuclei of crystallization were studied by concentration-dependent 1H NMR experiments and QTAIM analysis. Our findings showed that even with bulky substituents, the NH···OC interactions in most compounds played an important role in stabilizing the first nuclei formed during the crystallization process. However, in one case the molecular topology prevented the formation of NH···OC as the driving interaction in the first crystallization nuclei. In this case, the crystallization was mainly governed by a set of “weaker” interactions, showing that a subtle molecular change in the methylene spacer favored H···H interactions over directional N–H···O interactions. For some of the compounds studied, we propose both when the symmetry-independent molecules observed in the crystal lattice could be formed and when the water molecules are probably trapped during the crystallization to form the hydrate crystalline phases. This study contributes to the better understanding of issues related to modulating NH···OC hydrogen bonds using bulky substituents in the self-assembly of flexible TBU molecules.