Supramolecular crystalline structures were developed in films prepared from blends of a bio-based waterborne polyurethane (WBPU) based on castor oil/tartaric acid (CO-TA) with two different WBPUs synthesized from polycaprolactone diol (PCL) and dimethylol-propionic acid (PCL-DMPA) or TA (PCL-TA). Partial crystallization of the PCL segments generated topologies that strongly affected the final properties of the films. Depending on the internal emulsifier used in the synthesis of the PCL-based WBPUs and its proportion in the blend, the crystalline structures differed, resulting in lamellar, dendritic, or fiber-like networks. Several techniques were employed in the study: differential scanning calorimetry (DSC) to investigate the crystallization kinetics of the blends; optical and confocal microscopies to identify the topologies; positron annihilation lifetime spectroscopy (PALS) to correlate crystallinity with the mean nanohole volume, and dynamic mechanical analysis (DMA) to characterize the mechanical properties of the films. The crosslinked network from the CO-TA based WBPU and the microphase separation in the blends led to constrained crystal growth, resulting in distinct topologies. The work presents a novel approach to generate supramolecular structures, which had a positive effect on the films properties. The relationship between crystallinity and free volume, as measured by PALS, is also analyzed in terms of chain mobility.