Cocoa smoky off-flavor is due to inappropriate post-harvest processing and cannot be removed in the subsequent chocolate-manufacturing steps. To date, no reliable analytical method to detect key-analytes responsible for smoky off-flavor in incoming raw material is available. This study aims to develop an analytical method, suitable for quality control, to detect smoky markers. The cocoa volatilome was first profiled by headspace solid phase microextration combined with comprehensive two-dimensional gas chromatography-mass spectrometry from a set of representative smoky and non-smoky samples; advanced fingerprinting revealed the chemicals responsible for the off-flavor. The results served to develop a 1D-GC method suitable for routine application. Ten identified smoky markers were subjected to accurate quantification, thereby defining operative ranges to accept/reject incoming bean samples. On average, these markers are present in smoky samples at 7 to 125 fold concentrations vs. those in non-smoky beans, ranging from 32.5 ng/g for naphtalene to 721.8 ng/g for phenol.