Estimates suggest that by 2050 agricultural outputs must double to feed a growing world population and avoid food scarcity. At the same time, we must prepare crops to withstand climate change and develop more sustainable agricultural systems to reduce further harm to the Earth. Within this grand challenge, microbes are a promising source of solutions. Over one hundred products are available to farmers as commercial seed and/or soil amendments to increase plant health and decrease the use of exogenous chemical fertilizers. Unfortunately, existing products show highly variable performance and in general, mechanistic explanations for potential benefit are lacking. Even in the most promising cases, potentially beneficial microbes fail to colonize and persist within the context of complex agricultural soils. Enter – plant and microbial scientists! Our work aims to combine multiple experimental scales to identify novel, beneficial microbes, reveal their modes of actions and develop methods of increasing colonization and persistence of microbial consortia in complex systems.