Body mass has been shown to scale negatively with abundance in a wide range of habitats and ecosystems. It is believed that this relationship has important consequences for the distribution and maintenance of energy in natural communities. Some studies have shown that the relationship between body mass and abundance may be robust to major food web perturbations, fuelling the belief that natural processes may preserve the slope of this relationship and the associated cycling of energy and nutrients. Here, we use data from a long-term experimental food web manipulation to examine this issue in a semi-natural environment. Similar communities were developed in large experimental mesocosms over a six month period. Some of the mesocosms were then subjected to species removals, based on the mean strength of their trophic interactions in the communities. In treatments where the strongest interactors were removed, a community-level trophic cascade occurred. The biomass density of invertebrates increased dramatically in these communities, which led to a suppression of primary production. In spite of these widespread changes in ecosystem functioning, the slope of the relationship between body mass and abundance remained unchanged. This was the case whether average species body mass and abundance or individual organism size spectra were considered. An examination of changes in species composition before and after the experimental manipulations revealed an important mechanism for maintaining the body mass–abundance relationship. The manipulated communities all had a higher species turnover than the intact communities, with the highest turnover in communities that experienced cascading effects. As some species increased in body mass and abundance, new species filled the available size–abundance niches that were created. This maintained the overall body mass–abundance relationship and provided a stabilising structure to these experimental communities.