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Process-induced changes in thermo-mechanical viscoelastic properties and the corresponding morphology of biodegradable polybutylene adipate terephthalate (PBAT) and polylactic acid (PLA) blown film blends modified with four multifunctional chain-extending cross-linkers (CECL) were investigated. The introduction of CECL modified the properties of the reference PBAT/PLA blend significantly. The thermal analysis showed that the chemical reactions were incomplete after compounding, and that film blowing extended them. SEM investigations of the fracture surfaces of blown extrusion films reveal the significant effect of CECL on the morphology formed during the processing. The anisotropic morphology introduced during film blowing proved to affect the degradation processes as well. Furthermore, the reactions of CECL with PBAT/PLA induced by the processing depend on the deformation directions. The blow-up ratio parameter was altered to investigate further process-induced changes proving synergy with mechanical and morphological features. Using blown film extrusion, the elongational behavior represents a very important characteristic. However, its evaluation may be quite often problematic, but with the SER Universal Testing Platform it was possible to determine changes in the duration of time intervals corresponding to the rupture of elongated samples.