The cocoa bean shell (CBS) is a main by-product of cocoa processing, with great potential to be used as an ingredient for functional foods because of its nutritional and flavour properties. This study aimed to characterise and classify CBSs obtained from cocoa beans of diverse cultivars and collected in different geographical origins through their volatile profile assessed using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-qMS) and E-nose combined with principal component analysis (PCA). The study provides, for the first time in a representative set of samples, a comprehensive fingerprint and semi-quantitative data for >100 volatile organic compounds (VOCs), such as aldehydes, ketones, pyrazines, alcohols, and acids. Through PCA, a clear separation of the Criollo cultivar from the other cultivars was achieved with both GC-qMS and E-nose analytical techniques because of the high content of key-aroma VOCs. Several biomarkers identified by GC-qMS, such as 2-hepanol, 2-methylpropanoic acid, and 2,3,5-trimethylpyrazine, recognized as key-aroma compounds for cocoa beans, were found suitable for the classification of CBSs according to their quality and origin. GC-qMS and E-nose appeared to be suitable analytical approaches to classify CBSs, with a high correlation between both analytical techniques. The volatile fingerprint and classification of CBSs could allow for the selection of samples with a specific flavour profile according to the food application and, therefore, constitute an interesting approach to valorise this by-product as a food ingredient.