Aroma is a crucial criterion to assess the quality of apple fruits, juices, and ciders. The aim of this study was to explore similarities and differences in volatile profiles among apple fruits, juices, and ciders from different apple varieties (Festa, Branco, and Domingos) by headspace solid-phase microextraction gas chromatography–mass spectroscopy (HS–SPME/GC–MS). A total of 142 volatile organic compounds (VOCs) were identified, but only 9 were common in all analysed matrices and apple-tested varieties. Esters, alcohols, and aldehydes presented a higher concentration in apple fruits and juices, whereas esters, alcohols, and acids were dominant in ciders. Moreover, there were unique VOCs for each matrix and for each variety, highlighting the importance of the selection of apple varieties as an important factor to obtain good sensory and quality ciders, multiple benefits, and legal protection against the misuse of local products.