Organic farming systems receive organic amendments to maintain soil fertility and supply nutrients for plant growth. However, there is little information about the response of soil nitrogen (N) cycling functions and functional genes to different quality and quantity of organic amendments. This study investigated the effect of organic fertilizers (control, compost, and manure), and their interaction with cover crops (millet, buckwheat, and legume) on soil enzyme activities, N transformation rates and functional gene abundances under an organic production system. Organic N fertilizers had a stronger effect than cover crops on soil functions and functional gene abundances. Soil enzyme activities were increased by both compost and manure, but there was no difference between compost and manure for most enzymes. Nitrification potential, nitrite oxidation potential, and denitrification potential in manure treatment were significantly higher than those in control and compost treatment, indicating the application of manure had a higher N loss potential than compost application in this organic farming system. Organic N fertilizers significantly increased the abundance of genes encoding subtilisin (sub
), urease (ureC
), bacterial ammonia monooxygenase (amoA
), nitrite oxidoreductase (nxrB
), but had no effect on the abundance of genes encoding neutral metalloprotease (npr
), chitinase (chiA
or archaeal ammonia monooxygenase (amoA
). The activity of ammonia oxidizing bacteria and archaea were both increased by organic N fertilizers, and their activities were higher in manure treatment than those in compost treatment. Overall, the abundance of functional genes was significantly correlated with the corresponding enzyme activity. However, functional gene abundances were less important than soil biochemical properties to explain the variation in their corresponding enzyme activities.