In certified organic agricultural systems, soil nutrient status relies primarily on incorporation of organic matter and other specific inputs to meet requirements for phosphorus and micronutrients. Nutrient management strategies based on defined standards seek to maintain sufficient nutrient availability while minimizing potential losses. Although organic systems may result in lower levels of production than conventionally managed systems, sound soil nutrient management practices can minimize this gap. Certified organic standards are widely established globally, but traditional farming practices that resemble organic systems are also commonly used without adherence to a certified scheme. There is considerable debate about the efficiency of bio-amendments for use in organic farming due to their variability. Questions also persist about the sustainability of organic soil fertility management practices. The relevance of global variations among organic certification standards has not been a major consideration in research. Most soil improvement strategies focus on assessing the impact of particular amendments with less attention to a more holistic approach which integrates all components of the agricultural system. Research on implementation of practices based on certified organic standards highlights potential for multi–disciplinary, in-depth studies that identify combined impacts of organic management practices at a local scale. Standards developed at national level may not fully account for the breadth of soil types and environmental conditions. While soil improvement based on certified organic standards can contribute to socio-economic development and ecosystem services, local soil characteristics need to be considered in parallel with potential new avenues for sourcing nutrients, including organic matter management.