Certified organic agriculture stipulates a range of principles and standards, which govern farmer practices. The recent global expansion of organic agriculture has raised new challenges for organic agriculture, particularly whether management practices in organic farms are subject to the forces of conventionalisation. We studied changes in agroecological practices in certified organic farms in China, Brazil and Egypt. The study takes departure in the conventionalisation hypothesis and the analysis is framed using organic and agroecological principles. The study focuses on agroecological design principles, inherent to organic agriculture, of diversity in crop production, pest, disease and weed management, and soil fertility management. The research design was as a multiple case study of five cases in China, Brazil and Egypt. We show that the adoption of organic agriculture has induced fundamental changes in organic farmer management practices, although agroecological practices of organic farmers do not fulfil organic principles. The forces of conventionalisation exert a strong influence on changes in organic farmer practices. Organic ‘niche’ market crops with a high-value influence organic farmers’ management decisions, particularly regarding the prioritisation of diversity in the cropping systems for agroecological purposes. The farming systems have therefore not undergone major changes of their cropping patterns. Furthermore, there was a general heavy reliance upon input substitution for pest and soil fertility management. This study thus presents new data and a novel analysis of the implications at the farm scale of the global expansion of organic agriculture, and the influence of conventionalisation on farmers practices.