Food-web complexity and species richness are predicted to have tremendous effects on ecosystem functioning stability. Yet, our understanding of the relation between diversity and the stability of ecosystem functioning is still mainly limited to single trophic level communities and highly simplified food webs. To start filling this knowledge gap, we model allometric food webs and use structural equation modelling (SEM) to investigate the relations between diversity, food web structure and the temporal variability of total plant and animal biomasses and their components, i.e. synchrony and mean population variability. We find that stability responds differently depending on the metric used. When looking at total biomass variability, higher total biomasses and biomass stored at higher trophic level have the strongest stabilising effects, while species richness has lower impact than previously found. We confirm that synchrony among species is important for the stability of the total plant biomass. However, synchrony only weakly explains variations in the stability of total animal biomass among food webs. Species richness and food web variables often have opposite impacts on synchrony and mean population variability, leading to more ambiguous results for the plant community as synchrony matters only for plant stability. Our approach thus provides new insight on the complexity of the stability of ecosystem functioning in complex food webs.