Climate-driven changes in temperature and precipitation patterns are translating to greater challenges for agriculture in the Western US, especially for summer-irrigated crops such as processing tomatoes. Farming practices that focus on building soil health can help growers to adapt to and to mitigate the effects of climate change. One practice under much scrutiny is the use of non-native microbial inoculums, such as arbuscular mycorrhizae fungi (AMF), an obligate biotroph that forms symbiotic associations with plant roots. It is well established that AMF can provide benefits to both plants, enhancing nutrient uptake and drought resistance, and soil, contributing to aggregate stability and to the formation and storage of soil organic matter (SOM). Yet, the value of AMF inoculants as effective inputs for sustainable agriculture is still inconclusive and much debated. Soil management practices such as fertilization, organic amendments and cover crops can alter both native microbial populations and the potential impacts of a non-native AMF inoculum on plants and soil. Here, we investigate the effects of a non-native AMF inoculum on the agronomic and nutritional traits of processing tomatoes and soil health indicators across a long-term soil management gradient. In a split plot factorial field study across three years, mycorrhizal root colonization increased in plots treated with a commercial non-native AMF inoculant in the first year but dropped in subsequent years in both control and inoculated plots. In the final year of the study, inoculation with non-native AMF led to a decrease in root colonization compared to control plots. Additionally, inoculation with non-native AMF did not improve plant nutrient uptake, or tomato yields, but did significantly increase both the SOM and the C:N of rhizosphere soils in conventional (synthetic N), organic (cover crop and compost) and mixed (synthetic N and cover crop) systems. Finally, inoculation had greater impacts on rhizosphere microbial communities during vegetative growth and fruit set than at harvest. Although more research is required to determine the mechanisms through which rhizosphere SOM increased and persisted, this study suggests that non-native microbial inoculants can increase SOM in the short term; potentially priming soil communities and soil health and C storage pathways for longer term benefits.