There is an urgent need to develop predictive indicators of the effect of species loss on ecosystem functioning. Body size is often considered as a good indicator because of its relationship to extinction risk and several functional traits. Here, we examined the predictive capacity of species body size in marine and freshwater multitrophic systems. We found a significant, but weak, effect of body size on functioning. The effect was much stronger when considering the effect of body size within trophic position levels. Compared to extinctions ordered by body size, random extinction sequences had lower multiple species loss effects on functioning. Our study is the first to show experimentally, in multitrophic systems, a more negative impact of ordered extinction sequences on ecosystem functioning than random losses. Our results suggest apparent ease in predicting species loss effect on functioning based on easily measured ecological traits that are body size and trophic position.