In the last years, due to the increasing interest of consumers in natural products, market and industry choices were more directed towards the use of fragrances and flavors obtained from natural sources. Fermentation is a biological approach helpful to produce diverse aromatic compounds modifying precursors present in raw material, due to a wide array of extracellular enzymes which could be produced by microorganisms. Following this direction Lacticaseibacillus rhamnosus was employed as a starter for melon and orange by-products fermentation. Simple and vacuum distillation were applied for the recovery of the aromatic fraction and compared to identify the more promising in terms of aromatic profile composition. Detection and characterization of aromatic compounds were achieved using Head SpaceSolid Phase MicroExtraction Gas Chromatography–Mass Spectrometry (HS-SPME/GC–MS) approach. Fermentation led to interesting changes, increasing floral, herbal green and fruity notes. Overall, simple distillation allowed the greater recovery of aromatic compounds in terms of concentration for both substrates. This study highlights a possible strategy to produce complex distillates, composed of a mixture of aroma compounds, to be employed as additives in food, feed or perfumery industries as ingredients of natural origin.