Alternative transportation fuels (ATFs) can reduce air pollution. However, the influence of conventional fuels—diesel and gasoline, and particularly ATFs on photochemical air pollution is not well-characterized, limiting assessments of ATFs and air quality. This is mainly due to frequent use of lumped chemical mechanisms by related atmospheric modeling. Here we hypothesized that applying a chemical mechanism that is specifically developed according to both emission fractions and photochemical ozone creation potential of volatile organic compounds (VOCs) is key to gaining reliable insights into the impact of transportation fuels on photochemistry. We used a heterogeneous chemical mechanism with 927 reactions and relatively detailed emission inventories to specifically meet the requirements for reliable simulation of the effect of exhaust emissions from vehicles fueled by selected model fuels—diesel, gasoline, and mixtures of 15% gasoline with 85% ethanol (E85) or 85% methanol (M85)—on photochemistry. These dispersion-box model simulations revealed a strong influence of atmospheric background balance between VOCs and nitrogen oxides (NOX = [NO] + [NO2]) on the impact of exhaust emissions on photochemistry, with higher tendency toward ozone (O3) formation or destruction for more VOC-limited or NOX-limited conditions, respectively. Accordingly, higher [NOX]/[VOC] exhaust emission, such as from diesel and M85, resulted in lower O3, not only locally but also downwind of the emission. This offers a new perspective and measure for transportation fuel assessment. Rapid conversion of O3 to hydroxyl and hydroperoxyl radicals downwind of the exhaust emission indicates the importance of simulating the impact of road transportation on photochemistry at high spatial and temporal resolution. Peroxyacetyl nitrate formation was more sensitive to VOC emission under VOC-limited conditions than to NOX emission under NOX-limited conditions. Secondary formaldehyde dominated over primary emitted formaldehyde several minutes after emission. These findings should be verified using a 3D modeling study under varying meteorological conditions.