Essential oils (EO) are among the most important natural products, whose demand is ever spreading worldwide. The research towards newer bioactive components is one of the main goals of essential oil analysts, in light of the biological activity of the main volatile components. As a result, gas chromatography coupled to mass spectrometry (GC-MS) is a useful approach to determine the composition of the volatile fraction, alongside biological evaluation. In this concern, aiming to correlate the bioactivity and chemical composition, preparative gas chromatography (prep-GC) can be considered the technique of choice to isolate, and test target fractions from the column eluate. This approach represents a more reliable tool to “reconstitute” essential oil sub-fractions, avoiding the effective reconstitution of the essential oils by adding synthetic standards. In this study, in order to clarify the presence of target components responsible for the biological effect, a suitable prep-GC method was developed. In order to collect the highest amount of target fractions per analysis, wide bore capillary columns were exploited. From an analytical point of view, this approach allowed a consistent reduction in terms of total time analysis, thanks to the injection of undiluted EOs. In a first step, this system allowed the efficient isolation of essential oils’ sub-fractions, e.g monoterpenes and sesquiterpenes, to be tested with biological assays. Secondarily, according to the biological results, target components of each sub-fraction have been isolated by means of preparative multidimensional gas chromatography, in heart-cut mode, aiming to demonstrate potential synergic biological effects.