Trends in EU agricultural policies recognize an increasingly important role to biodiversity conservation and use in agroecosystems, including organic ones. However, along with their economic success, organic systems are facing a risk of ‘conventionalization’, i.e. the prevalence of input substitution over agroecologically-based crop management. Understanding what is functional agrobiodiversity and when it can be successfully applied in organics may help strengthen the recognition of organic farming as the reference management system for agricultural sustainability. Here functional agrobiodiversity is defined as a subset of total biodiversity identified at the gene, species or habitat level able to deliver a given agroecosystem service, which extent increases with diversity in the functional group. Different functional agrobiodiversity categories are identified, compared to biofunctionality, and used to illustrate the mechanisms through which they can support agroecosystem services and consequently sustainability. Three case studies taken from the author’s own research are used as examples to illustrate functional agrobiodiversity’s potential in organic systems as well as open questions. Results show that (i) functional agrobiodiversity has potential to support agroecosystem services but it is not possible to generalize the effects; (ii) a given functional biodiversity element may create conflicts between different target agroecosystem services. In those cases, prioritization of services is required.