Agrobiodiversity is declining and urgent actions are needed to reverse the ongoing loss of species and habitats that sustain food production-related ecosystem services. Farmers’ perceptions of agrobiodiversity could provide insights for improving policy designs towards more effective target setting for agrobiodiversity conservation and implementation measures. This scoping review identifies and synthesizes research on European farmers’ perceptions of agrobiodiversity. Using the PRISMA protocol, we identified 43 peer-reviewed scientific articles for qualitative analysis and aggregated these into three themes: 1) multiple agrobiodiversities, 2) agrobiodiversity loss and conservation, and 3) agrobiodiversity in society. The extant literature mainly associates with farmers’ perceptions of observable agrobiodiversity that has a mix of nature-centric and human-centric perspectives. The literature indicates that contradictions often arise from negative interactions or trade-offs between agrobiodiversity and farming when agrobiodiversity hinders farm production. Suggestions for future policies include considering farmers’ place-specific perceptions of agrobiodiversity; developing alternative principles to economically driven policy instruments; and investing in bringing public stakeholders closer to farmers through knowledge transfer and stakeholder collaboration.