Cross-contamination during pharmaceutical drug manufacturing can result in expensive recalls. To counter that, companies spend significant time and resources to ensure equipment cleanliness, often relying on the compound solubility data in various solvents as the main indicator of cleaning success. The aim of this work is to provide an alternative way to analyze the fouling and cleaning of surfaces in pharmaceutical manufacturing processes by using the quartz crystal microbalance with dissipation (QCM-D) and Raman spectroscopy. In this study, we chose an active pharmaceutical ingredient (API), sitagliptin phosphate monohydrate (SIT), as the model drug compound and observed its adsorption and desorption on stainless steel (SS2343), borosilicate glass (glass), and polytetrafluoroethylene (PTFE) surfaces. SIT was selected as the model API since it is a product manufactured on a large scale and is part of the widely used dipeptidyl peptidase-IV inhibitor class of oral hypoglycemics used to treat type 2 diabetes mellitus, while the chosen surfaces mimic the wall materials of manufacturing equipment and components such as reactors, transfer lines, and valves. Both the QCM-D and Raman spectroscopy results show the highest physisorption on PTFE, followed by SS2343 and glass. Additionally, QCM-D revealed a harder removal of SIT from SS2343 compared to glass and PTFE. Raman analysis of the chemical interactions disclosed C−F and C�O bond interactions between SIT and the surfaces, and the lack of a peak shift suggested dipole−dipole interactions. Furthermore, contact angle measurements indicate that hydrophobic attraction contributed to SIT adhesion to the PTFE surface. Subsequently, SIT coverage upon deposition on a PTFE surface has a significantly smaller surface area than on SS2343 and glass due to surface hydrophobicity, hence resulting in a longer removal time. These results provide a practical use of QCM-D and Raman spectroscopy to enhance the understanding of fouling and improve the cleaning of complex small molecules on relevant surfaces during the pharmaceutical manufacturing process.