In this study, an innovative methodology to optimize amorphization during the hot melt impregnation (HMI) process was proposed. The novelty of this report revolves around the use of thermal analysis in combination with design of experiments (DoEs) to reduce residual crystallinity during the HMI process. As a model formulation, a mixture of ibuprofen (IBU) and Neusilin was used. The main aim of the study was to identify the critical process parameters of HMI and determine their optimal values to assure a robust impregnation process and possibly the highest possible amorphization rate of IBU. In order to realize this, a DoE approach was proposed based on a face-centered composite design involving three factors. The IBU/Neusilin ratio, the feeding rate, and the screw speed were considered as variables, while the residual crystallinity level of IBU, determined using differential scanning calorimetry (DSC), was measured as the response. Additionally, the stability of IBU under HMI was analyzed using high-performance liquid chromatography to estimate the extent of potential degradation. In order to verify the correctness of the DoE model, tested extrudates were manufactured by HMI and the obtained extrudates were thoroughly examined using scanning electron micrography, X-ray powder diffraction, and DSC.