The number of flavour chemicals identified in coffee has reached over 1000 [1,2]. Coffee is one of the world's most popular beverages [3], highly studied for its health-related properties [4–6]. Studies on coffee associated with human health have focused on the negative aspects, such as the toxicity of caffeine [7,8]. Complex chemistry happens during coffee roasting and according to the literature, a number of compounds have been detected and quantified in coffee beans samples by UPLC–Q-TOF/MS [9–12]. The following method offers a simple approach for the qualitative and quantitative analysis of coffee bean extracts using a Waters Acquity G2 UPLC–Q-TOF/MS instrument adapted from the method by Kenny et al., [12]. The following modifications were made:•The method by Kenny et al. was developed on a triple quadrupole mass spectrometer, the below method was developed on a Q-TOF MS.•A combination of utilising both base peak index and mass extraction at 0.05Da allows for a sensitive, quantitative technique amidst poor background noise and poor separation with high mass accuracy (<5ppm).•By use of MSE centroid experiment, greater mass spectral information for metabolite profiling could be obtained.