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 the cost-effectiveness analysis of indicators. Moreover, the limited scientific literature available on indicator costs is based on ex-post analyses rather than on systematic data collection. The assessment of the costs of measuring biodiversity at the 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.