In this study, VOC profiles of acacia flowers and honey samples at different processing stages and related comb wax samples were studied using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry. It was found that some monoterpene compounds like α-pinene, myrcene, cis-β-ocimene, and 4-terpineol were common for acacia flower and all acacia honey samples, and the presence of verbenone and ocimene was first established in acacia honey. The most enriched VOC profile was obtained for raw honey before cell capping, where the final composition of lactones was achieved. On the contrary, number of alcohols, esters, and variety of terpenes, as well as their concentration in the honey samples decrease through ripening processes. Strained honey was characterized by the absence of camphor, α-bisabolol, and 3-carene, while isophorone and hexanoic acid were identified only in this type of honey. The composition of final VOC profile of honey was also influenced by the age of comb wax. The additional aromatic and lactone compounds, e.g., phenol, 1-phenylethanol, δ-hexalactone, and γ-heptalactone were observed for honey maturated in old dark comb wax.