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In the European Union (EU), the Common Agricultural Policy (CAP) is considered to be the critical public policy in terms of both impacts and funds dedicated to nature conservation, yet the goal of halting biodiversity loss in the EU remains elusive. The present paper examines the degree of biodiversity policy integration into the CAP and the quality of policy programming in a selected EU Member State in the 2014–2020 period. We use a heuristic model combining an assessment of biodiversity policy integration and a program theory analysis of the policy’s logic model. In addition, the elaboration of the logic model for other agricultural policy objectives, relevance and potential effects of measures and allocation of budgetary funds are evaluated for comparative purposes. The program logic model was found to be only loosely defined for most objectives of Slovenian agricultural policy. At the strategic level, the integration of biodiversity policy is limited to instruments that remunerate above-standard farming practices, investments and payments to areas with natural constraints. In contrast, the inclusion and consistency of biodiversity conservation in instruments supporting standard practices (e.g. direct payment schemes) is addressed only to a limited extent. Given their design and implementation, fewer than 10 % of relevant measures were judged to have strong or significant potential effects and will thus probably only partly meet the policy objectives. Finally, biodiversity conservation (estimated 5% of the total agricultural policy budget), as well as other environmental objectives (22–23 %), have a significantly lower priority than income- and production-related objectives (54–60 %). The future CAP should include adequate safeguards and incentives to improve the quality of programming and integration of biodiversity policy, particularly since an increasing emphasis is given to decision-making at the national level. However, although the post-2020 CAP programming system could, in principle, be seen as a step forward, there remains a high risk of underperformance in the field of biodiversity conservation in the EU Member States.