The ionome is the elemental composition of a tissue or organism. Phylogenetic variation in the ionomes of plant shoots has been widely reported based on controlled experiments, vegetation surveys and literature meta-analyses. However, environmental effects on phylogenetic variation in shoot ionomes have not been quantified. This study tests the hypothesis that phylogenetic variation in shoot ionomes is robust to environmental perturbation and that plant families can be distinguished by their shoot ionomes. Herbage was sampled from six subplots of the Rothamsted Park Grass Experiment. Subplots had received contrasting fertilizer treatments since 1856. Herbage was separated into its constituent species (n = 21) and concentrations of eleven mineral elements were determined in dried shoot material. Shoot concentrations of calcium (Ca), zinc (Zn), manganese (Mn), magnesium (Mg) and sodium (Na) showed significant variation associated with plant species, and responded similarly to fertilizer treatments in diverse plant species. Species x treatment interactions were indicated for phosphorus (P), potassium (K), nickel (Ni), copper (Cu) and iron (Fe). Plant families could be distinguished by their shoot ionomes. The most informative elements for discriminant analysis were Ca > Mg > Ni > S > Na > Zn > K > Cu > Fe > Mn > P. Whilst shoot ionomes were sensitive to fertilizer treatment, phylogenetic variation in a subset of the shoot ionome (Ca, Zn, Mn, Mg) was robust to this environmental perturbation.