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The relative effects of tree clearing, increased livestock densities and nutrient enrichment have rarely been compared across markedly different organism types, but negative effects are generally predicted. In contrast, adoption of rotational grazing is thought to benefit biodiversity in pastures but there are few supporting data. We examined the response of native plants, birds and reptiles to livestock management in south-eastern Australia. We selected 12 pairs of rotationally and continuously grazed farms. Two 1-ha plots were established in native pastures on each farm, one cleared and the second still retaining woodland tree cover. Stocking rates, fertilizer histories and landscape tree cover varied among farms. The abundance and richness of all taxa was lower in cleared pastures. The less mobile organisms (reptiles and plants) were positively correlated with tree cover at landscape scales, but only when trees were present at the plot scale. This pattern was driven by a few observations in landscapes with approximately 50% tree canopy cover. Neither bird abundance nor richness was correlated with stocking rates or nutrient enrichment, but plant richness responded negatively to both. The response of reptiles varied, declining with nutrient enrichment but positively correlated with livestock densities. These responses may be partly interpreted within the context of prior filtering of species pools through long-term grazing pressure. No taxa responded positively to rotational grazing management. We predict that reductions in livestock density and soil nutrients will directly benefit plants and less so reptiles, but not birds. Indirect benefits are predicted for birds and reptiles if management increases persistence of trees within paddocks. Although some forms of rotational grazing can increase woodland tree recruitment, rotational grazing in itself is unlikely to enhance diversity.