Our experiments addressed systemic metabolic effects in above-ground plant tissue as part of the plant’s response to the arbuscular mycorrhizal (AM) interaction. Due to the physiology of this interaction, we expected effects in the areas of plant mineral nutrition, carbon allocation and stress-related metabolism, but also a notable dependence of respective metabolic changes on environmental conditions and on plant developmental programs. To assess these issues, we analyzed metabolite profiles from mycorrhizal and non-mycorrhizal Lotus japonicus grown under greenhouse conditions at three different time points in the growing season in three different above-ground organs (flowers, sink leaves and source leaves). Statistical analysis of our data revealed a number of significant changes in individual experiments with little overlap between these experiments, indicating the expected impact of external conditions on the plant’s response to AM colonization. Partial least square-discriminant analysis (PLS-DA) nevertheless revealed considerable similarities between the datasets, and loading analysis of the component separating mycorrhizal and non-mycorrhizal plants allowed the defining of a core set of metabolites responsible for this separation. This core set was observed in experiments with and without mycorrhiza-induced growth effects. It corroborated trends already indicated by the significant changes from individual experiments and suggested a negative systemic impact of AM colonization on central catabolic metabolism as well as on amino acid metabolism. In addition, metabolic signals for an increase in stress experienced by plant tissue were recorded in flowers and source leaves.