Benzalkyldimethylammonium (or benzalkonium; BACs), alkyltrimethylammonium (ATMACs), and dialkyldimethylammonium compounds (DDACs) have been widely used for over six decades as disinfectants, especially during the COVID-19 pandemic. Here we describe methods for the determination of 7 BACs, 6 ATMACs, 6 DDACs, 8 BAC metabolites, and the structurally similar quaternary ammonium compound (QAC) herbicides diquat, paraquat, and difenzoquat in human serum and urine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methods were optimized using isotopically labelled internal standards and solid-phase extraction with weak cation-exchange cartridges. We separated diquat and paraquat chromatographically using a mixed-mode LC column, and BACs, ATMACs, DDACs, difenzoquat, and BAC metabolites using reversed-phase (C8 and C18) LC columns. Method limits of detection (MLODs) and quantification (MLOQs) were 0.002–0.42 and 0.006–1.40 ng/mL, respectively. Recoveries of all analytes fortified at 1, 5, and 20 ng/mL concentrations in serum and urine matrices were 61–129%, with standard deviations of 0–20%. Repeated analysis of similarly fortified serum and urine samples yielded intra-day and inter-day variations of 0.22–17.4% and 0.35–17.3%, respectively. Matrix effects for analytes spiked into serum and urine matrices ranged from –27% to 15.4%. Analysis of real urine and serum samples revealed the presence of several QACs in human serum. Although no parent BACs were found in urine, we detected, for the first time, several ω-hydroxy and ω-carboxylic acid metabolites of BACs at average concentrations in the range of 0.05–0.35 ng/mL. The developed method is suitable for application in large-scale biomonitoring of human exposure to QACs and their metabolites in human serum and urine.