The present research deals with the collection and structural elucidation of an unknown component, accounting for about 35% of the essential oil obtained upon distillation of the leaves of Eugenia uniflora L., harvested during summer (January, 2017) in Paraná State (Southern Brazil). A multidimensional gas chromatographic preparative system, based on the coupling of three GC systems equipped with apolar, PEG and ionic liquid-based stationary phases, was successfully applied for the isolation of the chromatographic band relative to the unknown molecule. The use of wide-bore columns allowed for an increased sample capacity compared to conventional micro-bore columns, thus the injection of a neat sample was feasible, greatly reducing the total collection time. A higher chromatographic efficiency was afforded by the use of a multidimensional approach in the heart-cut mode, exploiting the different selectivity of three stationary phases, which ensured the attainment of a highly pure fraction. In only five runs, more than 3 milligrams were collected, with an average purity greater then 95%. Finally, the unknown component was subjected to nuclear magnetic resonance spectroscopy, mass spectrometry and condensed phase Fourier-transform infrared spectroscopy, leading to the identification of 6-ethenyl-6-methyl-3,5-di(prop-1-en-2-yl)cyclohex-2-en-1-one. The presented approach has been demonstrated to be effective for the isolation and structural elucidation of unknown molecules in complex samples, which will allow for further in-depth studies, like biological evaluation or pharmacological tests.