This investigation is based on the automated solid phase microextraction GC-MS analysis of the volatile fraction of a variety of coffee bean matrices. Volatile analytes were extracted by headspace (HS)-SPME which was achieved with the support of automated instrumentation. The research was directed towards various important aspects relating to coffee aroma analysis: monitoring of the volatile fraction formation during roasting; chromatographic differentiation of the two main coffee species (Arabica and Robusta) and of a single species from different geographical origins; evaluation of the influence of specific industrial treatments prior to roasting. Reliable peak assignment was carried out through the use of a recently laboratory-constructed “flavour and fragrance” library and a dual-filter MS spectral search procedure. Further emphasis was placed on the automated SPME instrumentation and on its ability to supply highly repeatable chromatographic data.