Organic agriculture and organic food have expanded in recent decades but have undergone conventionalisation. Some claim that this contradicts some or all of the principles of ‘health’, ‘ecology’, ‘fairness’ and ‘care’ established by the International Federation of Organic Agricultural Movement (IFOAM). It is currently unclear how research on organic food/agriculture is structured, whether it embraces these principles, or how key crop diversification, driving sustainability, are addressed. To fill these knowledge gaps, we conducted a bibliometric analysis of 10,030 peer-reviewed articles published from 1945 to 2021 with topic and textual analysis. Our main findings were the following: (1) research is compartmentalised into scales and disciplines, with at field-scale ‘weed’, ‘soil’, ‘pest and disease’ management and ‘livestock farming’ seldom addressed together, or with environmental assessment separated from socioeconomic studies at farm scale. (2) The proportion of publications on ‘consumers’ preferences’ and ‘product quality’ research almost tripled in 20 years, from 10 to 27%, emphasizing the consumer orientation of research on organic agriculture and organic food. (3) Only 4% of articles covered all four IFOAM principles, while associated values such as ‘resilience’, ‘integrity’, ‘equity’, ‘transparency’ and ‘justice’ were even less frequently addressed. (4) Fewer diversification practices have been tested in organic than in conventional agriculture research, with fewer articles on ‘crop mixtures’ or ‘bee-friendly crops’ and a smaller range of legumes considered. (5) Research on genetic improvement and processing of organic legumes is lacking, which could constrain adoption of legumes in organic farming even more than in conventional agriculture. These results indicate a need for increasing interdisciplinary efforts at field level, with systematic measurement of multiple processes (weed-nutrient-pest dynamics). Future studies on organic agriculture should combine several diversification practices and legumes, with relevant indicators addressing the IFOAM values explicitly, and consider the whole value chain by linking producers with consumers.