Soil microorganisms have the potential to dramatically alter the nitrogen (N) availability in agricultural systems. It is unclear whether it is possible to manipulate microbes to enhance soil N availability and increase agricultural efficiency. Ideally, a management strategy would maximize the amount of soil ammonia and nitrate available to plants and decrease the amount lost through leaching or denitrification. To begin to address this strategy, we examined the abundance of key N-cycle genes in soils amended with different organic fertilizers. Apple root stocks were planted in fumigated organically and conventionally-managed orchard soils amended with one of five treatments: Brassica napus seed meal, B. napus seed meal with plant-based compost, plant-based compost, urea, urea with plant-based compost, and a no-treatment control. The abundance of aerobic ammonia-oxidation (AAO), denitrification and N-fixation genes in the rhizosphere were examined using quantitative PCR six weeks after amendment application. Bacterial and archaeal ammonia-oxidation gene abundance was significantly greater than other N-cycle genes in both organically and conventionally managed soil and in all treatments. In the organic soil, despite the N amendments, N-fixation genes were more abundant than denitrification genes. The fertilizer amendments had no effect on gene abundance in the organic soils. In conventional orchard soil, AAO gene abundance tended to be greater in the urea and B.napus amended soils. Denitrification genes were more abundant than N-fixation genes in the conventional soil, and were more abundant in the urea and B. napus soils, indicating a potential for greater loss of N from these soils. These preliminary data examined gene abundance; it remains to be determined whether these amendments are affecting the activity of N-cycling microbes. However, in conventionally-managed soils these amendments do alter the community composition of N-cycling soil microbes.