Atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) offers advantages as a rapid analytical technique for the quantification of three biomass degradation products (acetic acid, formic acid and furfural) within pretreated wheat straw hydrolysates and the analysis of ethanol during fermentation. The data we obtained using APCI-MS correlated significantly with high-performance liquid chromatography analysis whilst offering the analyst minimal sample preparation and faster sample throughput.