Organic agriculture is often deemed effective in conserving and promoting biodiversity, yet most studies have so far only focused on farmland in temperate areas and a few taxonomic groups, mainly birds and arthropods. Mediterranean agroecosystems host considerable biodiversity, and their wildlife likely delivers quantitatively important ecosystem services to agriculture, yet information is still limited. Here, we test the importance of organic farming and habitat structure for bat activity and richness in the Mediterranean. We disentangled the effects of organic vs. conventional management and habitat structure by adopting acoustic surveys and a matched-pair sampling design. Foraging bats preferred organic over conventional farming, with a scale-independent effect of local farm management on activity (but not richness), consistently across bat species and functional guilds. While fine-scale habitat structure had contrasting effects on bat species and guilds, the positive influence of linear landscape elements on bat activity was consistent and independent of management options. We highlight the key role of organic farming in preserving and promoting bat activity in agricultural areas, which brings the mutual benefit of sustaining bat conservation and emphasising the precious ecosystem services bats provide. To increase bat richness, however, appropriate management of landscape structure must be secured at larger geographical scales. •Foraging bats prefer organic over conventional farming.•Preference for organic farming is consistent across functional guilds of bats.•Landscape elements such as hedgerows and trees are key elements favoured by bats.•Bat richness is not influenced by farmland management.