Organic farming represents an integral part of agriculture in Austria. The share of organic holdings and the share of area being organically farmed are already high relative to other countries within the European Union. So far, analyses of the organic sector have mainly focused on the economic output and the utilised area; less is known about absolute crop yields per hectare and the gap between organic and conventional crop yields. Given their relevance for profitability calculations and production strategies, such data is of major interest for farmers, advisors, and decision-makers. To address this lack of knowledge, we combine the Austrian farm accountancy data and Integrated Administration and Control System data for Austria. This paper presents a statistical analysis of organic crop yield data for the national Austrian territory as well as for regional categories and covers the period from 2003–2016. The results show a significant difference in crop yields: i) between organic and conventional farming systems; ii) between regional categories in Austria. Organic cereals achieve 35% lower average crop yields than conventional systems, yields for organic root and tuber crops were 27–49% lower. Yield gaps of oilseed and protein crops vary widely between respective crop species.