Oxygenated polycyclic aromatic hydrocarbons (PAHs) often co-occur with their parent compounds and may be chemically more reactive due to increased hydrophilicity and polarity. However, the influences of oxygenated PAH on soil functions and involved microbes, for example, nitrification and ammonia-oxidizing microorganisms, are largely unknown. Benz(a)anthracene (BaA) and benz(a)anthracene-7,12-dione (BaAD) were selected to represent unsubstituted and oxygenated PAHs, respectively. A microcosm experiment was performed with an acidic agricultural soil following the ISO 14238 method. Each microcosm was spiked with varied concentration (1, 10, and 100 mg kg−1) of either pollutants, with the unamended as the control. Ammonium was added to all microcosms to stimulate soil nitrification. After 28 days of incubation, abundance and composition of both bacterial and archaeal amoA genes were determined using quantitative PCR and denaturing gradient gel electrophoresis (DGGE). In addition, the growth inhibition of an ammonia-oxidizing Thaumarchaeota by both PAHs were examined. Neither BaA nor BaAD suppressed soil nitrate production and reduced the abundance of ammonia-oxidizing archaea. DGGE analysis of archaeal amoA genes revealed the enrichment of a few I.1b Thaumarchaeota in the ammonium fertilized control treatment; however, no such succession was observed in all BaAD and in 100 mg kg−1 BaA microcosms. Ammonia-oxidizing bacteria appeared to be less responsive to the ammonium fertilization and PAH stress. The cultivation experiment indicated the growth of the archaeal enrichment YT7-2 was more sensitive to BaAD than to BaA. These findings indicate inhibitory potency of BaAD to soil ammonia-oxidizing I.1b Thaumarchaeota, thus implicating potential ecological risks of the widely occurred oxygenated PAHs.