A new approach for the analysis of diesel engine fuel filters has been developed. This method involves minimal to no sample preparation, allowing rapid and unbiased analysis of diesel fuel filters. In recent years, diesel fuel filter plugging incidences have increased in parallel with changing emissions legislation. Fuel filter blockages can result in increased emissions, reduced efficiency, and engine failure. It is not fully understood why fuel filter blockages occur; as a result, there has been an international increase in research into the cause of fuel filter plugging. The method discussed in this paper utilizes a thermal desorption (TD) style sample introduction technique that can be used in conjunction with gas chromatography−mass spectrometry (GC-MS) and presents a fast, simple, and more sustainable approach to the analysis of fuel filters. When required, an efficient and straightforward sample cleanup process was developed and was used to simplify and improve confidence in the data identification and assignment; this method is up to three orders of magnitude faster than some procedures adopted in the literature. Further complementary analytical techniques, such as ultrahigh-performance supercritical fluid chromatography−mass spectrometry (UHPSFC-MS) and high-resolution GC-MS, were used to access additional sample-specific information. This new approach has been successful in the identification of problematic materials deposited on blocked fuel filters, concurrent with recent research. This information can aid in the development of mitigation strategies to combat fuel filter plugging.