Organic farming and other agri-environmental schemes (AES) are important policy tools to support environmental-friendly agriculture. Often, AES require a direct reduction of actual management intensity to sustain biodiversity and non-marketable ecosystem services. In addition to lower management intensity, differences in topography and soils between AES and non-AES land can occur, driven by the targeted placement of AES in the landscape. Many of the latter effects of an AES are, however, widely unknown and frequently ignored, limiting a comprehensive understanding of how organic farming and other AES deliver environmental outcomes. We analysed pedological, topographical and other spatial characteristics of parcels under two grassland AES, i.e., organic farming (vs. conventional) and extensive management (vs. intensive). Thus, this study assessed whether organic farming is related to differences in topography and soil conditions in both extensively and intensively managed grasslands in the study region in the north of Switzerland. Therefore, we combined a regional-scale spatial analysis of permanent grassland parcels and a soil survey. Both AES were tested not only in interaction with each other but also within the two main harvest types, i.e., meadows (mainly mown) and pastures (mainly grazed), resulting in eight distinct grassland types that were studied. Results show both AES to be linked to differences in soil nutrients as well as topographical and other spatial characteristics. We found interactions of the two AES with the harvest type, i.e., meadow versus pasture. This was particularly pronounced for extensively managed conventional meadows, which were frequent at low elevation and on land potentially suitable for arable farming. Extensively managed pastures and all organic grasslands exhibited reduced production conditions (i.e., higher elevation, steeper slope, lower soil phosphorus concentrations). Yet, differences between organic and conventional grasslands were by tendency more pronounced in intensively than extensively managed grasslands. Our results show that farmers preferentially adopted both AES on land not ideal for intensive production, with the exception of many extensively managed meadows in low elevations. Our study therefore demonstrated that an assessment of the ecological outcomes of an AES must not only account for direct effects via management restrictions but also for indirect effects via spatial targeting by farmers. More research is still needed to assess and compare direct and indirect effects of AES to support evidence-based policymaking and improve spatial targeting of different land-use types.