Semi-arid alpine ecosystems on the Tibetan Plateau are experiencing rapid climate change and extensive anthropogenic activity, concomitant with the encroachment of shrubs. Shrub encroachment leads to changes in both the structure and functioning of semi-arid alpine steppes. Yet, the encroaching impacts of shrubs on the above- and belowground ecosystem functioning of the semi-arid alpine steppes remains uncertain. To quantify shrub encroachment impacts on ecosystem functioning of the semi-arid alpine steppes, two shrub encroached alpine steppe sites are investigated, with one site encroached by a leguminous shrub ( Caragana spinifera) and another site encroached by a non-leguminous shrub ( Dasiphora fruticosa). Results showed that following both Leguminosae and Non-Leguminosae shrub encroachment, not only do these alpine steppes greatly increase the individual ecosystem functions but that this included significant enhancing of the ecosystem multifunctionality (EMF). We concluded that the main impacts of shrub encroachment were to facilitate belowground EMF (BEMF) rather than aboveground EMF (AEMF) in alpine steppes. Our findings also highlight that soil nutrients play critical roles in driving ecosystem functioning responses to shrubs encroachment. These findings further our understanding of shrub encroachment impacts on ecosystem functioning of the Tibetan semi-arid alpine steppes.