Quaternary ammonium compounds (QACs) are a class of antimicrobial disinfectants whose use in cleaning products increased during the COVID-19 pandemic. Chemically, their low vapor pressure indicates a proclivity to persist on surfaces, and their presence suggests a level of protection against microorganisms. The widespread application of QACs in response to the SARS CoV-2 virus created a need to evaluate their longevity on surfaces, for both efficacy and possible health risks. There are however, no standardized analytical methods for QAC surface sampling and analysis, and no published studies quantifying their concentrations on mass transportation vehicles-a high occupancy, close-contact microenvironment documented to facilitate the spread the SARS CoV-2 virus. Here, we describe a robust liquid chromatography mass spectrometry (LC-MS) method for the analysis of QACs and simultaneous development of a direct surface sampling and extraction protocol. We demonstrate the applicability of the method through the analysis of surface samples collected from in-service public transportation buses.The rapid, sensitive LC-MS method included 8 target QACs quantified on a Q-Exactive HF Hybrid Quadrupole-Orbitrap mass spectrometer using an electrospray ionization source and Dionex UltiMate 3000 UHPLC system for analyte separation. QAC standard mixtures at concentrations between 0.1 ng mL−1 and 2000 ng mL−1 were analyzed, and chromatographic separation of all analytes was achieved in less than 10 min. All correlation coefficients were reported at r > 0.986, and LODs ranged from 0.007 to 2.103 ng mL−1 for all compounds, confirming the method's sensitivity. A previously reported surface sampling and extraction protocol was modified to further simplify the procedure and expand the number of target compounds. The new sampling protocol was optimized from 10 commercially available wipes and 4 solvent types by quantifying recovery from the surface. Band-Aid brand small gauze pads saturated with isopropanol had the highest recovery efficiencies, ranging from 61.5 to 102.9% across all analytes. To test the real-world applicability, wipe samples were collected from 4 in-circulation New Jersey Transit buses on 5 separate days over the course of a month to assess the occurrence and longevity of QACs on sanitized mass transportation vehicles. Concentrations of QACs were detected on every wipe sample taken, and at all sampled time points, confirming their persistence on hard surfaces. QACs have the potential to form polymers, and detection of the polymer might serve as a secondary indication of their effectiveness on surfaces. None of the polymers detected however, were unique to QACs from this study. The polymers detected were already present in the wipe and used as an internal standard to demonstrate the efficacy of extraction and analysis of polymeric QACs.