The diel variation of meteorological conditions strongly influences the formation processes of secondary air pollutants. However, due to the complexity of sampling highly reactive chemical compounds, significant information about their transformation and source can be lost when sampling over long periods, affecting the representativeness of the samples. In order to determine the contribution of primary and secondary sources to ambient levels of polyaromatic hydrocarbons (PAHs) and quinones, measurements of gas and PM1 phases were conducted at an urban site in the Guadalajara Metropolitan Area (GMA) using a 4-h sampling protocol. The relation between PAHs, quinones, criteria pollutants, and meteorology was also addressed using statistical analyses. Total PAHs (gas phase + PM1 phase) ambient levels ranged between 184.03 ng m−3 from 19:00 to 23:00 h and 607.90 ng m−3 from 07:00 to 11:00 h. These figures both coincide with the highest vehicular activity peak in the morning and at night near the sampling site, highlighting the dominant role of vehicular emissions on PAHs levels. For the gas phase, PAHs ranged from 177.59 to 595.03 ng m−3, while for PM1, they ranged between 4.81 and 17.44 ng m−3. The distribution of the different PAHs compounds between the gas and PM1 phases was consistent with their vapour pressure (p °L) reported in the literature, the PAHs with vapour pressure ≤ 1 × 10−3 Pa were partitioned to the PM1, and PAHs with vapour pressures ≥ 1 × 10−3 Pa were partitioned to the gas phase. PAHs diagnostic ratios confirmed an anthropogenic emission source, suggesting that incomplete gasoline and diesel combustion from motor vehicles represent the major share of primary emissions. Quinones ambient levels ranged between 18.02 ng m−3 at 19:00–23:00 h and 48.78 ng m−3 at 15:00–19:00 h, with significant increases during the daytime. The distribution of quinone species with vapour pressures (p °L) below 1 × 10−4 Pa were primarily partitioned to the PM1, and quinones with vapour pressures above 1 × 10−4 Pa were mainly partitioned to the gas phase. The analysis of the distribution of phases in quinones suggested emissions from primary sources and their consequent degradation in the gas phase, while quinones in PM1 showed mainly secondary formation modulated by UV, temperature, O3, and wind speed. The sampling protocol proposed in this study allowed obtaining detailed information on PAHs and quinone sources and their secondary processing to be compared to existing studies within the GMA.