This work analyzes the differences in the final properties of two waterborne polyurethanes (WBPU) prepared with two macrodiols of different chemical structure, but similar molecular weight, as well as the variations caused by incorporating low percentages of microfibrillated cellulose nanocrystals. One of the polyurethanes was based on a synthetic but biodegradable precursor (polycaprolactone diol, PCL) and a second one based on a bio‐based macrodiol derived from castor oil (CO1). The bio‐based material presented higher mechanical properties at room temperature than the synthetic one, with the Young's modulus (MPa) ranging from 2.23 ± 0.09 to 84.88 ± 0.96 for the PCL and bio‐based WBPUs, respectively. Additionally, the PCL‐based WBPU showed to be more sensitive to the incorporation of cellulose than the bio‐based WBPU, and it also suffered changes during time due to delayed crystallization. The behavior of the two systems were compared and related to the different structure of the macrodiols that led to different interfacial interactions. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 44207.