<p>Biodegradable pseudo-proteins (PPs), a novel class of synthetic polymers mimicking natural proteins, offer unique advantages for biomedical applications, including superior biocompatibility, tuneable degradation, and structural versatility. In this study, we investigate the mechanical and microstructural behavior of two representative PPs—poly(ester amide) (PEA) and poly(ester urea) (PEU)—using a novel in situ stretching technique combined with nanobeam wide-angle X-ray scattering (WAXS). This advanced methodology enables real-time, submicron-resolution analysis of molecular ordering during mechanical deformation. For both PEA and PEU, the WAXS patterns two distinguished (001) and (010) peaks associated with lamellar stacking and chain–chain packing of aliphatic segments, correspondingly. Our results reveal that PEA, characterized by higher crystallinity of the (010), exhibits brittle fracture under stress, whereas PEU demonstrates elastic behavior due to its lower (010) crystalline content and greater chain mobility. These findings establish a direct correlation between sectional crystallinity and mechanical performance, providing valuable insights for the rational design of PPs with tailored properties for biomedical use.</p>