In this study, the levels of polycyclic aromatic compounds (PACs), such as polycyclic aromatic hydrocarbons (PAHs) and their oxygenated derivatives (oxy-PAHs) were investigated in guarana seeds (Paullinia cupana) subjected to different drying methodologies. An innovative extraction method combined with a miniaturized dispersive solid-phase extraction cleanup procedure was developed for the determination of PACs concentration. Thirteen-eight guarana seed samples subjected to three different drying methodologies (sun drying, greenhouse drying, and alguidar furnace drying) were collected from different rural producers in the South Region of the State of Bahia, Brazil. Principal component analysis and diagnostic ratios were used to evaluate the correlation between samples and the PACs and the main sources of contamination. According to the results, the average concentration of PACs found in sun-dried, greenhouse-dried, and alguidar-dried ranged from 1.30 µg kg−1 (coronene) to 114 µg kg−1 (fluorene), from 0.48 µg kg−1 (dibenzo[a,h]anthracene) to 128 µg kg−1 (fluorene), and from 6.0 µg kg−1 (anthracene) to 422 µg kg−1 (phenanthrene). Oxy-PAHs, such as 1,4-NQ was detected predominantly in sun-dried and greenhouse-dried samples at concentrations ranging from 30.7 µg kg−1 to 83.9 µg kg−1. Low molecular weight PAHs, such as naphthalene, acenaphthylene, and fluorene were found in most of the samples independently of drying methodology. However, high molecular weight PAHs, including the carcinogenic benzo[a]pyrene was found predominately in alguidar-dried samples in concentrations higher than 20 µg kg−1.