1. Organic farming has potential for the conservation of global biodiversity and associated ecosystem services. Despite this, knowledge of the effects of organic farming systems on farmland biodiversity is limited in Asia, the worldwide leader in rice production. 2. We conducted the first national-scale study to investigate the effects of three different rice farming systems (conventional, low-input, and organic) and specific management practices (e.g. herbicide and insecticide applications, crop rotation, and levee-vegetation management) on species richness and abundance of multiple taxonomic groups (plants, invertebrates, Pelophylax and Hyla japonica frogs, cobitid loaches, and birds) in Japan during 2013–2015. 3. Organic fields supported the highest richness and abundance of several taxonomic groups (native/Red List plants, Tetragnatha spiders, Sympetrum dragonflies, and Pelophylax frogs), followed by low-input and conventional fields. We also found taxon-specific responses to specific management practices. For instance, plant richness and Tetragnatha and Sympetrum abundance increased with reduced herbicide and/or insecticide applications. Sympetrum and Cobitid loach abundance increased in the absence of crop rotation, whereas H. japonica abundance increased with crop rotation. Pelophylax abundance increased with an increased height of levee vegetation. 4. At spatial scales larger than single fields, waterbird richness and abundance were positively correlated with the proportion of organic rice fields, presumably due to increased prey abundance. Meanwhile, landbird richness and abundance were positively associated with annual precipitation and annual mean temperature, suggesting that such climate increases food availability. 5. Synthesis and applications. We highlight the positive effects of organic and low-input farming for biodiversity relative to conventional farming in rice-paddies. We also provide the scientific basis of the current agri-environmental schemes in Japan, subsidising organic and low-input farming for biodiversity. The taxon-specific associations with management practices indicate that avoiding crop rotation, maintaining levee vegetation, and organic farming at large spatial scales can also be wildlife-friendly. These practices may thus be incorporated into agri-environment schemes for effective biodiversity conservation.