Value of the data •These are the first data on the contents of VOCs in CBSs from different origins and cultivars determined by HS-SPME/GC-qMS •The dataset allows the selection of CBSs with specific flavor characteristics according to the food application •The present data contribute to the chemical characterization and add-value of this cocoa by-product as food ingredient •The data can be used for reference of volatiles quantification and allow other researchers to extend the statistical analysis •The datasets from both techniques GC-qMS and E-nose may be useful for developing rapid detection methods for CBS origin and cultivar authentication