We report a previously undescribed seed-storing behavior of banner-tailed kangaroo rats (Dipodomys spectabilis) that reduces losses to microbes. D. spectabilis cuts upper stems of the grass Sporobolus cryptandrus into 3- to 5-cm sections that we refer to as seed stems. Seeds within these seed stems remain attached to their rachis and are protected by an enveloping leaf. Most seed stems are bundled together tightly in packs of about 50 to several hundred individual stems and jammed vertically into cul-de-sacs excavated in the walls of their burrows. This behavior reduces rate of infection of seeds by fungi and also may reduce number of seeds pilfered by arthropods. Furthermore, compared with seeds of S. cryptandrus housed in middle sections of seed stems, those housed in the ends had a higher rate of infection. Simulated seed stems of wheat straw containing seeds of white millet (Panicum miliaceum) had a lower rate of infection and fewer species of fungi than seeds only protected by wire mesh. Seeds closer to the top of the simulated seed stems were more likely to be infected and had more species of fungi. Community structure and dynamics of microfungi also appeared affected by the protective layering of seed stems. We suggest that D. spectabilis manages the structure, and perhaps dynamics, of communities of microbes within their food caches by modifying position, location, or organization of food items.