Technical Abstract: Brassica tissues are often promoted as a soil amendment to meet various management objectives, particularly in organic production systems. To predict the efficacy of brassicaceae seed meal amendments as either biofumigants or organic fertilizers, a better understanding of the impacts of seed meal amendment on resident soil microbial communities is warranted. This study analyzed the influence of high (Brassica juncea) and low (Brassica napus) seed meal glucosinolate content in addition to myrosinase inactive derivatives on soil microbial community function with respect to nitrogen cycling. All seed meal amendments examined stimulated NO generation in an orchard soil. N-mineralization and nitrification were temporarily inhibited in response to B. juncea seed meal application but the inhibition was dependent upon myrosinase activity and corresponding generation of allyl isothiocyanate. Microbial communities responded differentially to seed meal amendments: nematodes were enhanced by seed meals with either low glucosinolate or no myrosinase activity, fungi were stimulated by low glucosinolate seed meal, and changes in bacterial abundance were not significantly different from the control. Apart from changes in overall abundance, nematode diversity was also modified in response to seed meal amendment and differed between the stimulatory amendments. Collectively, these results indicate that microbial communities and overall soil function respond differentially to both seed meal type/glucosinolate content and isothiocyanate generation.