Increased demand for certified organic products has led to an increase in the number of certified organic farms in developing countries. Knowledge of farmer nutrient management practices on certified organic farms in developing countries is limited. Thus, the aim of this study was to investigate the impact of the adoption of certified organic agriculture on farm nutrient flows and nutrient budgets, and evaluate to which degree organic farms comply with organic principles relating to nutrient management. The study is based on five case studies of different types of certified organic farming systems in Brazil, Egypt and China. Farm nutrient flows and nutrient budgets for nitrogen, phosphorous and potassium were created for each farm. Four of the five organic systems studied had nutrient surpluses on the farm budget. The surpluses were of varying magnitude. The main difference between organic and non-organic farm nutrient flows was the replacement of mineral fertilizers with organic inputs. However, the magnitude of nutrient flows were generally similar for organic and non-organic farms. Certified organic farms with positive nutrient budgets had a heavy reliance on external inputs. Continued high dependence on an external supply of nutrients, which typically originate from mineral sources, poses a significant challenge to organic farmers’ fulfilment of the principles of organic agriculture.