Automatic lay-up and in-situ consolidation with thermoplastic composite materials is a technology under research for its expected use in the profitable manufacturing of structural aeronautical parts. This study is devoted to analysing the possible effects of thermal degradation produced by this manufacturing technique. Rheological measurements showed that there is negligible degradation in PEEK for the temperatures reached during the process. Thermogravimetric analysis under linear heating and constant rate conditions show that thermal degradation is a complex process with a number of overlapping steps. A general kinetic equation that describes the degradation of the material with temperature has been proposed and validated. Attenuated total reflectance Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy confirmed that there is no remarkable degradation. The use of a combination of in-situ and ex-situ experimental techniques, including kinetic modelling, not only provides reliable information about degradation but also allows setting optimal processing conditions.