Provisioning ecosystem services play a vital role in sustaining human well-being. Agro-ecosystems contribute a significant share of these services, besides food and fodder and also fuel and fibre as well as regulating and cultural ecosystem services. Until now, the indication of provisioning ecosystem services of agro-ecosystems has been based almost only on yield numbers of agricultural products. Such an indication is problematic due to several reasons which include a disregard of the role of significant anthropogenic contributions to ecosystem service co-generation, external environmental effects and strong dependence on site conditions. We argue for an enhanced indication of provisioning ecosystem services that considers multiple aspects of their delivery. The conceptual base for such an indication has been made by prior publications which have been reviewed. Relevant points were taken up in this article and condensed into a conceptual model in order to develop a more holistic and expanded set of indictors, which was then exemplarily applied and tested in three case studies in Germany. The case studies represent different natural conditions, and the indicator set application showed that ecosystem services (ES) flow—in terms of output alone—does not characterise agro-ecosystems sufficiently. The proposed aspects of provisioning ecosystem services can give a fuller picture, for example, by input-output relationships, as it is possible by just using single indicators. Uncertainties as well as pros and cons of such an approach are elaborated. Finally, recommendations for an enhanced indication of provisioning ecosystem services in agro-ecosystems that can help to integrate agricultural principles with ideas of sustainability and site-specific land use are derived.