This data article describes the analysis of volatile organic compounds (VOCs) in 44 samples of cocoa bean shells (CBS) obtained from cocoa beans of diverse cultivars and collected in different geographical origins. The volatile compounds were extracted by headspace solid-phase microextraction (HS-SPME) method and then analyzed by gas chromatography coupled to a quadrupole mass spectrometry GC-qMS. The retention times, identification and semi-quantification of 101 VOCs are reported. Data collected on the volatile profile of CBS samples using E-nose analysis are also available. Additional data related to physicochemical characteristics and color analysis for CBS samples are reported. Further interpretation and discussion on these datasets can be found in the related article entitled “Assessment of volatile fingerprint by HS-SPME/GC-qMS and E-nose for the classification of cocoa bean shells using chemometrics” (Barbosa-Pereira et al., 2019).