Within the world of natural food supplements, organic extracts deriving from young plant meristematic tissue (bud-derivatives) are becoming attractive, thanks to their richness in bioactive molecules. This natural source is scarce, but every year, tons of plant material, including buds, come from city pruning. If this sustainable source is rather promising from a circular economy point of view, the safety of the obtained supplements must be assessed. In fact, anthropic microcontaminants, such as polycyclic aromatic hydrocarbons (PAHs), could adsorb onto the urban buds, leading to a possible contamination of the bud-derivatives. In this study, we developed a magnetic dispersive solid phase extraction (m-dSPE) based on molecularly imprinted microparticles, combined with GC-MS, to quantify the 16 priority PAHs in such extracts. The D-optimal experimental design was implemented to maximize analytes’ recovery with the smallest set of experiments. The optimized method was characterized by great selectivity thanks to the molecular imprinted polymer and ease of use provided by m-dSPE. Moreover, it complies with green principles, thanks to the minimum consumption of organic solvent (1.5 mL of acetone per sample). The recoveries ranged from 76 to 100% and procedural precision was below 10% for most PAHs. Despite the matrix complexity, low quantification limits (0.7–12.6 μg kg−1) were reached. This guaranteed the PAHs’ quantitation at levels below those indicated as safe by a European Community regulation on food supplements. None of the analyzed samples, coming from different anthropically impacted areas, showed concerning PAHs levels.