Organic and low-input farming practices are considered keystones for the conservation of biodiversity in semi-natural systems. Accordingly, attention to the assessment of the benefits stemming from these activities is increasing in order to provide a solid base for the adoption of agro-environmental incentives and to support their monitoring and evaluation. The evaluation of the positive effects of organic and low-input farming activities on biodiversity is limited mainly by: the difficulty in proposing simple and widely-applicable indicators of biodiversity, and the substantial lack of data concerning the costs of measuring biodiversity - an essential element for a cost-effectiveness analysis. Moreover, the limited scientific literature available is based on ex-post analysis rather than on systematic data collection. The assessment of the costs of measuring biodiversity at farm-scale throughout Europe is one of the specific tasks of the BioBio project (UE-FP7). In this work, we discuss methodological aspects and preliminary results based on data gathered during fieldwork measurements of biodiversity in BioBio.