A rapid non-derivatisation gas chromatographic (GC) method for quantification of palmitic, stearic and oleic acids was achieved using a flame ionisation detector and a highly polar capillary column at elevated temperature. These long chain fatty acids (LCFA) can accumulate in anaerobic digesters and a simple extraction method was also developed to permit a more rapid sample turn-around time, facilitating more frequent monitoring. The GC method was satisfactory in terms of peak separation, signal response, reproducibility and linearity range. The extraction method achieved recoveries of 103.8, 127.2 and 84.2% for palmitic, stearic and oleic acid respectively. The method was tested on digestate from mesophilic laboratory-scale digesters fed with source-segregated domestic food waste, and showed good repeatability between replicate samples. It was observed that the concentrations of stearic and palmitic acid in digesters routinely supplemented with trace elements were lower in proportion to the applied lipid loading than those without supplementation.