Fused filament fabrication (FFF), an additive manufacturing technique, is used to produce prototypes and a gradually more important processing route to get final products. Due to the layer-by-layer deposition mechanism involved, bonding between adjacent layers is controlled by the thermal energy of the material being printed. Thus, it is strongly in conjunction with the temperature development of the filaments during the deposition sequence. This study gives out an in-process set-up enabling to record temperature profile of two adjacent filaments or a sequence of deposition in various locations during FFF process. The main characteristic of the presented procedure is the possibility of obtaining a global temperature profile resulted from an IR-camera; parallel to those recorded using a K-type thermocouple. Needless to say that a K-type thermocouple accurately records the local temperature at the interface of adjacent filaments. Conversely, an IR-camera signifies the temperature profile on the captured surface. The obtained results showed that there is a remarkable difference between the cooling rate and re-heating peaks. The primary outcome of this study is the consideration of results accuracy and the possibility of working on optimization of the obtained temperature profile. Altogether it helps optimize inter-layer strength while assessing the temperature evolution.