The functional influence of native mammalian herbivores on ecosystem functions is declining as they get gradually replaced by domestic livestock who have become the predominant herbivores across the world. Alongside rewilding, restoration, and conservation, it is now important to address whether livestock can maintain erstwhile functions of the native herbivores they have displaced across the world's grasslands, savannas, and steppes. If yes, this has implications for the future of biodiversity, ecosystem functions and services, food-security, and other social and environmental dimensions. We test competing alternative hypotheses with a replicated, long-term, landscape-level experiment to ask whether livestock in the Trans-Himalayan ecosystem can match decadal-scale soil-C sequestration in soils under native herbivores. Over decadal time-scale (2006-16) livestock were imperfect substitutes since they could only attain three-fourths of the total soil-C stocks under native herbivores. Structural equation models supported the hypotheses that livestock alter soil microbial communities towards lower fungal abundance, which is detrimental for microbial carbon use efficiency (CUE) and for soil-C storage. This lag between livestock and native herbivores can be addressed through microbial restoration and rewilding of soil. Therefore, the idea of functional substitutability must be leveraged alongside microbial rewilding to restore and conserve ecosystem functions. Together they can reconcile conflicting demands from food-security and ecosystem services, and should become an integral part of nature-based climate solutions.