The understanding of the polymer composition–properties relationship is of great importance to improve the mechanical properties of bio-based polyurethanes containing long chain fatty acid derivatives. In this work, water-borne poly(urethane urea) dispersions containing dimer fatty acid-based diisocyanate (DDI), ethyl ester l-lysine diisocyanate (EELDI), 1,4:3,6-dianhydro-d-glucitol (isosorbide, IS) and dimethylolpropionic acid (DMPA) residues were prepared. The investigation focuses on the thermal and mechanical properties of these dispersion-cast films as well as on the morphology in correlation with the polymer composition. Significant dependencies of these properties and the morphology on the polymer composition are observed. By partially replacing the flexible DDI with the rigid EELDI as well as by increasing the isosorbide contents in the monomer feed, the Tg as measured by DSC was significantly enhanced from 18 to 58 °C (1st Tg) and to above 70 °C (2nd Tg). As evidenced from the DSC, AFM and FT-IR measurements, the H-bonds-induced micro-phase separation was influenced by the polymer composition. The observed improved phase mixing at relatively high EELDI-to-DDI ratio was related to the increased EELDI content and the corresponding urethane/urea bonds. The viscoelastic behavior of these dispersion-cast films showed a strong dependence on the ratio of the flexible DDI to the rigid EELDI and were less dependent on the IS and DMPA contents.