The benefits of low input farming on biodiversity and ecosystem services are already well-established, however most of these studies focus only on the focal field scales. We aimed to study whether these benefits exist at the whole farm scale, to find the main environmental driving effects on biodiversity at the whole farm scale in farms of different grassland grazing intensity, applying three well-known species diversity indicator groups of different ecological traits.Edaphic (earthworms), epigeic (spiders) and flying (bees) taxa were sampled in each identified habitat type within 18 low-input farms in Central Hungary, 2010. The number of habitat types, the number of grassland plots, the cumulative area of grasslands and habitat type had an effect on the species richness and abundance of spiders, while grassland grazing intensity influenced the species richness of bees. Both bees and spiders were sensitive to vegetation and weather conditions, resulting in more bees on flower-rich farms and those having higher temperature; and more spiders on farms with more heterogeneous vegetation structure and in low-wind areas. Relatively few earthworms were found in the whole study, and their abundance was not influenced by any of the farm composition and management variables.We conclude that local field management (grazing intensity of grassland patches) can have a farm scale effect, detectable on species diversity indicators that have high dispersal ability and strong connection to grasslands as important foraging sites (bees). However, other farmland biota (spiders) is also strongly determined by farmland composition and habitat diversity, therefore the maintenance of a mosaic within-farm habitat structure is strongly recommended. The application of earthworms as farmland composition or management indicators is strongly restricted because of their special needs of soil conditions.