Farmers hoping to manage cropping systems sustainably are turning to cover crops to help mitigate plant pathogens. Plants with biofumigant properties are used to control soil-borne pathogens in agricultural settings, especially in till systems, where the brassicas are incorporated into the soil as green manure or seed meal. The effect of these crops is not well studied in no-till systems; thus, it is hard to know if they are as effective as green manure. Whether or not these cover crops can effect changes during a single growth season has not yet been studied. This study compared the response of the soil microbial community to four different brassica cover crops, two of which are commonly used in vineyards (Sinapis alba L. (white mustard) and Raphanus sativus (L.) Domin (tillage radish)) as well as two brassicas that are native or naturalized to the Okanagan (Capsella bursa-pastoris (L.) Medik. (Shepherd’s purse) and Boechera holboelli (Hornem.) Á. Löve and D. Löve (Holbøll’s rockcress)). Cover crops did not affect fungal species richness, but B. holboelli recover crops were associated with increased evenness among fungal taxa. Both C. bursa-pastoris and S. alba had lower levels of plant parasitic nematodes compared to non-brassica controls. These results were apparent only after a single growing season, which indicates growers could use this approach as needed, minimizing long-term exposure to biofumigants for beneficial soil microbes.