Chios Mastic Gum (CMG) and Chios Mastic Oil (CMO) are two unique products of the tree Pistacia lentiscus var. Chia, cultivated exclusively on the Greek island of Chios. In the present study, the method proposed by the European Pharmacopoeia for mastic identification was employed using HPTLC together with an in-house method. A GC-MS methodology was also developed for the chemical characterization of CMOs. α-Pinene and β-myrcene were found in abundance in the fresh oils; however, in the oil of the aged collection, oxygenated monoterpenes and benzenoids such as verbenone, pinocarveol, and α-campholenal were found at the highest rates. Additionally, the antimicrobial activity of Chios Mastic Gums (CMGs) with their respective Chios Mastic Oils (CMOs) was evaluated, with growth tests against the fungi Aspergillus nidulans, Aspergillus fumigatus, Candida albicans, Mucor circinelloides, and Rhizopus oryzae, and the bacteria Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis, with the samples exhibiting a moderate activity. To our knowledge, this is the first time that an HPTLC method is proposed for the analysis of mastic and its essential oil and that a standardized methodology is followed for the distillation of CMO with a parallel assessment of the ageing effect on the oil’s composition.