In anaerobic digestion (AD), long-chain fatty acids (LCFAs) produced by hydrolysis of lipids, exhibit toxicity against microorganisms when their concentration exceeds several millimolar. An absorption detection system using a quartz crystal microbalance (QCM) was developed to monitor the LCFA concentration during an anaerobic digester’s operation treating oily organic waste. The dissociation of the LCFAs considerably improved the sensor response and, moreover, enabled it to specifically detect LCFA from the mixture of LCFA and triglyceride. Under alkaline conditions, the frequency-shift rates of the QCM sensor linearly increased in accordance with palmitic acid concentration in the range of 0⁻100 mg/L. Frequency changes caused by anaerobic digestate samples were successfully measured after removing suspended solids and adjusting the pH to 10.7. Finally, the QCM measurements for digestate samples demonstrated that frequency-shift rates are highly correlated with LCFA concentrations, which confirmed that the newly developed QCM sensor is helpful for LCFA monitoring in terms of rapidness and usability.