The desertification paradigm has a long history in the Sahel, from colonial to modern times. Despite scientific challenge, it continued to be influential after independence, revived by the dramatic droughts of the 1970s and 1980s, and was institutionalized at local, national and international levels. Collaborative efforts were made to improve scientific knowledge on the functioning, environmental impact and monitoring of selected agricultural systems over the long term, and to assess trends in the ecosystems, beyond their short term variability. Two case studies are developed here: the pastoral system of the arid to semi-arid Gourma in Mali, and the mixed farming system of the semi-arid Fakara in Niger. The pastoral landscapes are resilient to droughts, except on shallow soils, and to grazing, following a non-equilibrium model. The impact of cropping on the landscape is larger and longer lasting. It also induces locally high grazing pressure that pushes rangeland resilience to its limits. By spatial transfer of organic matter and mineral, farmers’ livestock create patches of higher fertility that locally enhance the system’s resilience. The agro-pastoral ecosystem remains non-equilibrial provided that inputs do not increase stocking rates disproportionately. Remote sensing confirms the overall re-greening of the Sahel after the drought of the 1980s, contrary to the paradigm of desertification. Ways forward are proposed to adapt the pastoral and mixed farming economies and their regional integration to the context of human and livestock population growth and expanding croplands.