Modern agriculture faces conflicting objectives—increasing agricultural production while preserving and fostering biodiversity. As intensive agricultural management threatens biodiversity, legal obligations aim to halt biodiversity loss and safeguard threatened species. In Switzerland, agricultural priority species have been defined to set environmental goals for biodiversity, with limited success so far. This study spatially defines farmland focus zones with potential for the promotion of priority species for conservation in agricultural landscapes. We overlaid information about field-level impact of agricultural activities using the Swiss Agricultural Life Cycle Assessment (SALCA-BD) as “impact of agricultural activities” with the potential distribution of Swiss priority birds. The potential distribution was assessed by aggregating predictions from species distribution models of 27 bird priority species. We identified significantly high/low values for management impact and potential distribution using hotspot analyses. Multivariate clustering was used to identify zones that should be preserved (low management impact, high bird potential) and zones where conservation measures could be promoted (high management impact, high bird potential). Zones which were minimally impacted by management and had a high potential for birds included grassland with structures, covering ca. 18% of the studied farmland. Zones with high management impacts consisted mainly of arable land with little structures, covering ca. 31% of the studied farmland, occurring mainly in the Swiss lowlands. Our results help to assess and visualize the intertwined links between agricultural management and the species inhabiting these agricultural landscapes in a spatially explicit manner. This can help to identify zones and regions for ecological promotion and set priorities for action within future agricultural policies.