Small mammals can influence grassland assembly by selecting against palatable plants – the community can become dominated by the plants they avoid. This predation-based selection could have indirect effects on community biomass and tissue quality, especially given how untasty plants may have higher concentrations of recalcitrant carbon compounds including lignin. We tested small mammal effects on biomass and tissue quality of roots and shoots in a two-year-old 18 ha restored tallgrass prairie with established zones of high and low plant predation. We focused on the three dominant herbaceous functional groups of tallgrass prairie (perennial forbs, C3 and C4 grasses), and targeted the early stages of assembly given that plant predation by small animals can unfold quickly and is difficult to subsequently quantify. We predicted rodent predation to create communities with reduced biomass but an increased abundance of lignin-rich plants; we only observed the former. Rodents reduced aboveground biomass by 46% but preferentially targeted lignin-rich plants, with the latter result explained by the predominance of granivory over herbivory – there was no opportunity for selection based on tissue palatability. Based strictly on aboveground biomass, we estimated small mammals reduced standing stocks of recalcitrant carbon by 65 kg ha −1 , with reductions in belowground stocks almost certainly higher given that root:shoot ratios averaged 21:1. Given that the quantity and quality of plant production can affect ecosystem functions including decomposition and the regulation of soil carbon stocks, our work suggests that non-random plant predation may substantially affect rates of soil carbon accumulation in the early stages of grassland development.