Agricultural intensification drives biodiversity loss and shapes farmers' profit, but the role of legacy effects and detailed quantification of ecological-economic trade-offs are largely unknown. In Europe during the 1950s, the Eastern communist bloc switched to large-scale farming by forced collectivization of small farms, while the West kept small-scale private farming. Here we show that large-scale agriculture in East Germany reduced biodiversity, which has been maintained in West Germany due to >70% longer field edges than those in the East. In contrast, profit per farmland area in the East was 50% higher than that in the West, despite similar yield levels. In both regions, switching from conventional to organic farming increased biodiversity and halved yield levels, but doubled farmers' profits. In conclusion, European Union policy should acknowledge the surprisingly high biodiversity benefits of small-scale agriculture, which are on a par with conversion to organic agriculture.