Under the EU’s new “Farm to Fork” strategy, crop production systems should rapidly become more environmentally friendly. In particular, by adopting agroecological measures that support functional biodiversity and improve ecosystem services for crop production, this paper contributes to the ongoing efforts in characterizing the socio-economic effects that the upscaling of these measures entails, by looking into two key measures: flower strips and mulching. One important socio-economic aspect of their adoption is their potential impact on agricultural income; however, knowledge on costs and benefits of measures enhancing functional biodiversity at the farm level is still limited. In order to improve these shortcomings our approach makes use of data from field experiments completed with interviews to provide cost–benefit results for flower strips and organic mulching. The estimations show that for “flower strips,” on average costs could be covered by compensation payments. Regarding the in-crop measure “organic mulching,” the benefits potentially outweigh the costs under the frame conditions of organic agriculture. The analysis also highlights some obstacles and knowledge gaps in the estimation of benefits, especially for off-crop measures like flower strips.