Plants are negatively affected by aluminum (Al) in acidic soils (pH ≤ 5.0), which impairs root growth and ultimately plant yield. Organic acids are closely related to Al neutralization improving the metal tolerance with an expansive metabolic cost. Here, we investigated phenotypic, metabolic, and genetic responses of three Arabidopsis thaliana ecotypes, Columbia (Col-0), Wassilewskija (Ws) and Landsberg erecta (Ler) in response to Al. By comparing the respective control plants with Al-exposed plants, the ecotypes Col-0 and Ws displayed stronger reductions in root growth and reproductive yield than Ler. All ecotypes presented high expression of ALMT1, an Al-resistance associated gene. Further analyses revealed a large accumulation of diverse amino acids, carbohydrates and organic acids following Al stress in both shoot and root tissues of Col-0 and Ws plants, but not in Ler. Altogether, our results suggest that a higher capacity for using and translocating reduced carbon molecules seems crucial to overcoming Al stress in the Ler ecotype. In addition, lower expenses in carbon molecules might be linked to a higher capacity to deal with Al stress, supporting a tight relationship between primary metabolism and Al stress responses. Finally, novel insights on the influence of Al over plant growth and primary metabolism in both shoots and roots are described.