This research demonstrates the feasibility of active thermography in inspecting 3D printing filaments. Examine the potential of pulsed phase thermography in quality assurance of short and natural fibre reinforced polymer composites. Signal analysis scripts were built in Matlab to process the raw data recordings collected. These scripts included were; Single Pixel Analysis (SPA) that consisted of 2D wavelet denoising and single pixel plotted through time; Thermal Signal Reconstruction (TSR); and Pulsed Phase Thermography (PPT) that implemented the inbuilt with Fast Fourier Transform (FFT). 3D printed natural fibre composites offer sustainable and cost-effective solutions to material challenges. When considering combining natural fibres and 3D printing there are several manufacturing challenges that must be overcome. The focus of this research is to ascertain if active thermography is a suitable tool for online inspection of fibre reinforced filaments used for 3D printing composites. The aim of the inspection is to identify fibre rich and fibre poor regions along the filament, where uniformly distributed fibres and heating along the filament are preferred. Regions with a locally high weight percent of fibres, known as a fibre bunch, can cause problems when used to print a part resulting in a waste of materials and failed print jobs. The paper presents a feasibility study showing the potential of using pulsed thermography to identify fibre bunching. An external heating stimulus is applied to the sample and an infrared detector is used to monitor the thermal decay. The thermal contrast produced by fibre bunches compared to regions of uniformly distributed fibres is used to identify potential problem areas and provide a means of quality control. Investigation includes variation of the heating stimulus, data collection and data processing routines. Flat bottom holes (FBH) and notches of the samples were easiest to detect, filaments mixed with fibres and salt were more challenging and difficult to detect, which will require further investigations.