Agroforestry can help to conserve biodiversity and enhance multiple ecosystem services such as carbon sequestration, microclimate regulation and nutrient cycling. However, in land planning and biodiversity certification schemes it remains difficult to quantify the effect of agroforestry on biodiversity across time and space. Here we combine insights from a second‐order meta‐analysis, a stakeholder questionnaire, and a review of biodiversity assessment tools to establish a route towards more accurate estimates of agroforestry effects on biodiversity. Via a synthesis of cross‐taxa meta‐analyses, we evaluated the impact of agroforestry and landscape structure on biodiversity. Complementing the literature evidence, we performed a stakeholder questionnaire to determine the perceptions and preferences of stakeholders with regards to biodiversity. The meta‐analyses synthesis indicates predominantly positive or no effects of agroforestry practices on biodiversity, albeit with contextual nuances such as landscape structure and system design. The questionnaire revealed stakeholders' recognition of biodiversity's pivotal role in agroecosystems and a willingness to support methods to assess the effects of agroforestry on biodiversity. There was a preference for user‐friendly, web‐based tools that integrated mapping features and checklists tailored to diverse agroforestry types. Finally, we evaluated 73 existing biodiversity tools in terms of their capability of incorporating agroforestry components. The tools' review revealed limitations in terms of their specificity, accessibility or capacity to encompass multifaceted agroforestry designs. Our three‐faceted approach provided comprehensive insights about the building blocks required to develop an evidence‐based and user‐friendly tool for predicting the effects of agroforestry on biodiversity. Specifically, our interdisciplinary synthesis underscores the potential of agroforestry in promoting biodiversity while emphasizing the need for an evidence‐based, user‐centric tool to effectively assess biodiversity within agroforestry systems, accounting for landscape context and system design. Such a tool should be constructed with input data for different agroforestry types, across taxa and updateable when knowledge gaps are filled.