Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California’s Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0–5, 5–15 and 15–30 cm.