Land degradation, and particularly soil fertility decline, poses a serious threat to crop production in Sub‐Saharan Africa (SSA) because of an increasing pressure on land to meet the increasing demand for food caused by the growing population. In order to overcome the prevalent food insecurity and to eradicate poverty among smallholder farmers, there is a need for a paradigm shift in managing soil fertility by seeking options that optimize crop production per unit area through sustainable intensification (SI) in the face other drivers affecting productivity, including climate change. Sustainable intensification also includes the need to ensure that soil‐related ecosystem services other than the production of food, feed, and fiber are retained. In recent years, Integrated Soil Fertility Management (ISFM) has formed the basis of many initiatives aiming at intensifying agriculture in Africa. ISFM is defined as a ‘set of soil fertility management practices that necessarily include the use of fertilizer, organic inputs, and improved germplasm combined with the knowledge on how to adapt these practices to local conditions, aiming at maximizing agronomic use efficiency of the applied nutrients and improving crop productivity. All inputs need to be managed following sound agronomic principles’. While ISFM has been shown to increase crop productivity and input use efficiency in short term trials, its longer term impacts on soil health and yield stability remain largely unknown. There is a need to invest in long‐term observatories to understand the processes associated with ISFM, its sustainability and identify the conditions for reversing soil degradation. Such long‐term field trials also facilitate the optimization of ISFM across different cropping systems as affected by agro‐ecological conditions and other drivers of change such as climate change. A group of scientists met in Kampala Uganda in November 2013 to discuss a strategy for a coordinated effort to establish long‐term observatories for important cropping systems in relevant agro‐ecological zones in SSA. The strategy is based on the establishment of multi‐locational core and satellite trials along relevant agro‐ecological, soil type, and degradation gradients. Core trials will omprise a full suite of ISFM treatment combinations, across the different cropping systems, and will run for relatively long periods of time (at least 10 years). Satellite trials will be smaller and shorter term (minimum 3 years) and will comprise a sub‐set of ISFM factors included in the core trials and their combinations. Satellite trials will evaluate ISFM components that can be used as entry point to maintain productivity on non‐degraded lands and ehabilitate degraded lands whereas core trials will be used to assess the long‐term impact of ISFM (i) on soil health, yield stability, and sustainability, and (ii) on rehabilitation of highly degraded lands. Key indicators of sustainability and provision of ecosystem services such as soil organic carbon (SOC), soil biodiversity, nutrient and water balances, yields and yield stability, and weed and pest dynamics will be monitored. The research team will include scientists with expertise in fields relevant to this initiative, including agronomy, soil science, agroecology, biometrics, simulation modeling, GIS, and socio‐economics. Capacity building is an important component of the initiative, thus the team will actively engage postgraduate students at local and international (i.e. foreign) universities. Site selection will be aided by GIS to target the different cropping systems on representative soil types in the agro‐ecological regions where the crops are generally grown. The initiative will consider densely populated areas where there is a greater need for SI. An pen source database will be developed to enhance data management and sharing of information among the stakeholders in the different countries. Quantitative synthesis of data obtained from the trials will be handled with tools such as meta‐analysis which are robust. Modeling and GIS tools will be used to extrapolate data, to extend the inference space under different environmental conditions where ISFM performs. It is expected that these long‐term observatories will provide a meaningful contribution to resolving the challenge of SI of smallholder farms in sub‐Saharan Africa.