Granivory and soil disturbance are two modes by which burrowing rodents may limit the success of native plant restoration in rangelands. This guild of animals has prolific effects on plant community composition and structure, yet surprisingly little research has quantified the impact of rodents on plant restoration efforts. In this study, we examined the effects of seed removal and soil disturbance by the giant kangaroo rat (Dipodomys ingens) on native plant restoration in a California rangeland. Using experimental exclosures and stratifying restoration plots on and off rodent-disturbed soil, we assessed the individual and combined effects of seed removal and soil disturbance on seedling establishment of four native plant species. Across all species, biotic soil disturbance by kangaroo rats reduced seedling establishment by 19.5% (range = 1–43%), whereas seed removal reduced seedling establishment by only 6.7% (range = 4–12%). Rates of seed removal across species weakly paralleled kangaroo rat dietary preferences. These results indicate the indirect effects of burrowing rodents such as kangaroo rats on native seedling establishment via changes in soil properties may rival or exceed the direct effects of seed removal.