This publication highlights the effect that different chain extenders (CEs) have on the structure–property relationships of soy‐based polyurethanes that have been exposed to hydrolytic degradation for 480 and 960 h at 80°C. Gel content, crosslinking densities, surface energy, atomic force microscopy, dielectric, and dynamic mechanics were used for monitored structural changes. Polyurethanes (PU) is composed of a structure with minor phase separation when a chain extender is not used, maintaining all properties over time. However, when a chain extender, butane‐1.4‐diol (BDO), ethane‐1.2‐diol (MEG) our (2‐hydroxypropoxy)‐propane‐2‐ol are added, it is noted that there is a more significant degradation in the flexible domains, modifying the fraction between the initial rigid (HS)/soft (SS) segment that makes the polymer stiff and brittle. The hydrolysis degradation generates new Fourier transform infrared bands relative to urea (1640 cm−1) and amide (1800 cm−1). The reduction in band intensity of the C=Ofree at 1730 cm−1, while increasing the intensity of C=Obonded at 1710 cm−1 indicated a higher phase separation degree. After 960 h the TgS decreased, while the TgH was practically unchanged. The higher polarization observed in the PUs with BDO and MEG samples indicates the increased phase separation resulting in hydrolytic degradation.