Block-copolyesters of polyethylene terephthalate (PET) and polyethylene naphthalate (PEN) were synthesized via reactive extrusion. The influence of processing parameters on the material properties on a molecular scale like degree of trans-esterification, block length, and degree of randomness were investigated. The varied process factors were extrusion temperature and rotational speed. The effects of process parameter variation were investigated by 1 H-NMR-spectroscopy. The experimental results show a clear dependence of the molecular properties on the processing conditions. By using statistical experimental design (DoE), it was possible to prepare defined copolyesters from PET and PEN without addition of further chemicals. With a degree of randomness between 0.05 and 0.5, the presence of an actual copolyester was confirmed when appropriate extrusion conditions were applied. The reactive extrusion process was confirmed to be suitable to produce defined block-copolyesters in a predictable and reproducible way. It was possible to produce designed sequence lengths, which could be adjusted within a range of 11-136 repeating units in the case of PET and, in the case of PEN, of 2.5-26. The produced materials can be used as barrier materials or barrier coatings to protect substrates against molecular oxygen and water vapour, e.g., in organic photovoltaic applications or food packaging. The described method is a one-pot alternative method to the previously described chemical recycling pathway.