Poly[R-3-hydroxybutyrate-co-(R-3-hydroxyvalerate)] (PHBVs) are promising biopolymers, which could substitute petro-based plastics for packaging applications. To anticipate the behavior of PHBVs when transformed using conventional thermo-mechanical shaping processes, it is needed to better understand the effect of processing temperature on their crystallization behavior and final properties. The objectives of the present work were thus (1) to better understand the influence of the processing temperature on the PHBV macromolecular and crystalline structures, depending on its HV content, and (2) to define a processing window guaranteeing optimized mechanical properties of PHBV films. An innovative experimental strategy was proposed, enabling the study of melting and crystallization events, crystalline structure changes, and evolution of mechanical properties of PHBV according to processing temperature, using identical thermal cycles. A comprehensive dynamic monitoring of the studied PHBVs was achieved by coupling differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), step scan DSC (SDSC), observations of isothermal crystallization under polarized optical microscopy (POM), thermo-regulated wide angle X-ray analysis (WAXS), Nuclear Magnetic Resonance (NRM), and finally mechanical tests on PHBV films. The combination of these experiments revealed how inappropriate processing temperatures can result in irreversible changes in PHBVs’ macromolecular and crystalline structures, thermal behavior and mechanical performances. When increasing the HV content of the copolymer, adjusting the processing conditions according to these results revealed to be critical to match the functional properties targeted for a specific use.