Human-wildlife conflict poses a significant challenge to 21st-century conservation, with a limited understanding of these interactions within the broader social and ecological context of coexistence. Specifically, the impact of large-scale refaunation efforts on social-ecological dynamics in landscapes shared by humans and wildlife remains poorly understood. This study aims to enhance this understanding by jointly analyzing the consequences of refaunation involving wildlife and cattle in a mixed-use landscape in sub-Saharan Africa. Applying an interdisciplinary approach encompassing ecology, soil science, agricultural economics, and environmental anthropology, we reconstruct the coupling processes in social-ecological systems triggered by refaunation over the last five decades in Namibia's portion of the Kavango-Zambezi Transfrontier Conservation Area (KAZA TFCA). To assess ecological impacts of refaunation with cattle or elephants, space-for-time substitutions are used. The findings demonstrate that post-1960s increases in cattle numbers, and the surge in wildlife numbers since the 1990s have shaped the coexistence landscape. Elephant refaunation positively impacted herbaceous vegetation and soil conditions at intermediate elephant densities but negatively affected vegetation at higher densities. Wildlife refaunation, achieved through conservation and tourism, reduced income inequality. However, this effect was outweighed by the concentration of wealth among affluent cattle owners. Increasing rural inequality contributed challenges of local resource governance. Our study highlights that refaunation has profound ecological and socio-economic repercussions, challenging existing forms of resource governance in KAZA-TFCA and similar coexistence landscapes in Africa, and emphasizing the need for further research on the simultaneous increase of wildlife and cattle and its socio-ecological consequences.