Fused Filament Fabrication (FFF) is presently one of the most commonly used Additive Manufacturing (AM) technology for various engineering applications. However, accuracy and stability remain a major challenge during AM processes. FFF is inherently a thermal process. So, it is important to analyze and monitor the temperature evolution of each deposited filament during and after printing. This work presents an in-situ temperature measurement setup with an infrared camera, used in collecting temperature profiles of printed layers. These temperature profiles were compared to a theoretical 1D heat transfer model, demonstrating good agreement between the two sets of data. The temperature measurement experiment has been repeated for different printing process parameters, namely print speed, flowrate, and bed temperature. The effect of fan cooling is also studied. These data play a significant role in determining the optimal settings needed to achieve the desired bonding between adjacent filaments. This can be concluded by studying the effect of changing the parameters on the cooling of each deposited filament concerning the material’s glass transition temperature. The average temperature of any two adjacent layers in a part has been evaluated and compared to the material’s glass transition temperature to provide a better insight on the quality of adhesion taking place. A visual inspection of the part has also been proven to be useful in evaluating the effect on the final quality.